AceView: Gene:HHLA1, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView.

Expression: According to AceView, this gene is expressed at low level, only 9.2% of the average gene in this release. The sequence of this gene is defined by 13 GenBank accessions from 11 cDNA clones, some from blastocyst (seen once), pluripotent cell line derived fromblastocyst inner cell mass (once), teratocarcinoma (once). We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 17 distinct gt-ag introns. Transcription produces 3 alternatively spliced mRNAs. There are 3 probable alternative promotors (see the diagram). The mRNAs appear to differ by truncation of the 5' end, presence or absence of a cassette exon, overlapping exons with different boundaries.
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant bAug10).
Function: There are 2 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to a disease (Translocation, Genetic). Proteins are expected to localize in various compartments (nucleus, extracellular region).
Protein coding potential: The 3 spliced mRNAs putatively encode good proteins, altogether 3 different isoforms (1 complete, 1 COOH complete, 1 partial).

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12

Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
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cDNA accession Links to the sequence	Tissue most 5' clones in red	Match mRNA	From bp to bp in mRNA	From bp to bp in accs.	Clone encodes complete protein (with AA variation)	Features	Anomalies detected by AceView	Accession match over (% length)	Base differences relative to genome (% identity)
AF110315	teratocarcinoma	.b	1 to 2268	8 to 2275	L247S	tiling clone,		2268/2290 (99 %)	4 diff (99.9 %id)
AK022619		.a	2085 to 4105	1 to 2021		tiling clone, available from FLJ,		2021/2021 (100 %)	5 diff (99.8 %id)
DV080717	pooled	.a	264 to 925	1 to 662		tiling clone,		662/664 (99 %)	9 diff (98.7 %id)
DV080718	pooled	.a	478 to 1129	652 to 1		tiling clone,	Submitted on the opposite strand	652/654 (99 %)	7 diff (99.0 %id)
EG328194	pooled	.a	80 to 484	1 to 404				404/404 (100 %)	4 diff (99.1 %id)
EG328195	pooled	.a	32 to 443	412 to 1		tiling clone,	Submitted on the opposite strand	412/469 (87 %)	2 diff (99.6 %id)
CX760803	Blastocyst, pluripotent cell line derived fromblastocyst inner cell mass	.c	1 to 698	30 to 724	W113X P120L W121X P130T G131X ...	tiling clone,	Submitted on the opposite strand	695/801 (86 %)	3 diff (99.7 %id)
NM_001145095.1		.a	1 to 4105	1 to 4105	exact	RefSeq,		4105/4105 (100 %)	0 diff (100 %id)
AU124948		.a	2086 to 2881	2 to 795		capped		794/798 (99 %)	4 diff (99.5 %id)
AU148706		.a	3649 to 4105	457 to 1				457/457 (100 %)	0 diff (100 %id)
TI_985974676		.a	559 to 1163	614 to 9		tiling clone, fully sequenced,		606/614 (98 %)	3 diff (99.6 %id)
TI_985974677		.a	238 to 1172	13 to 942		tiling clone, fully sequenced, AAA		930/942 (98 %)	24 diff (97.5 %id)
Z14310. matches multiple genes		.a	238 to 1172	13 to 942		tiling clone,	This clone was ignored, also hits gene OC90	930/942 (98 %)	24 diff (97.5 %id)
Z14310. matches multiple genes		Gene OC90, variant not shown					This clone was ignored, also hits gene OC90