RetrogeneDB ID: retro_hsap_2924

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:42031237..42032052(+)
• Located in intron of: ENSG00000014824

Retrocopy information

• Ensembl ID: ENSG00000249212
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATP1B1
• Ensembl ID: ENSG00000143153
• Aliases: ATP1B1, ATP1B
• Description: ATPase, Na+/K+ transporting, beta 1 polypeptide [Source:HGNC Symbol;Acc:804]

Sequence

>retro_hsap_2924
AAAGCCAATGAGGAGGGCAGTTGGAAGAAATTCTTCTGGAACTCAGAGAAGAAGGAGTTTTTAGGCAGGACTGGTGGCAG
TTGGTTTAAGATCATTCTATTCTACATAATATTTTATGGCTGCCTGACTGGCATCTTCATCGGAATGATCCAAGTGGTGC
TGCTCACCATCAGTGAATTTAAACCCACATATCAGAACCACATATCAGGACCCCCACCAGGATTAACACAGATTTCTCAG
ATCCAGCAGACTGAAATTGCCTTTCATCCTAATGATCCCAAGCACTGTGAGGCATATGTGCTGAACGTAGTTAGGTTCCT
GGAAAAGTACAAAGATTCAGCCCAGAAGGATGACATGATTTTTGAAAATTGTGACAATGTGCCCAGTGAACCCAAAGAAC
GAGGAGACTTTAATCAAGAATGAGGTGAGCGAAAGTCTGCAGATTCAAGCTTGAGTGGCTGGGAAATTGCTCTGGATTAA
ATGACAAAACTTACAGCTACGAAGAGGGCAAACCACATGTTATTATAAAGCTCAAGTGAGTTCTAGGCTTCAAACCTAAG
TCTCCCGAGAATGAGTCCTTGGAGACTTACCCAGTGATGAAGTATAACGCATCTGTGTTTCCTGTTCAGTGCACTGGCTA
GCAAGATGAAGATAAGGATAAAAATAGAAATGTGGAGTATTTTGGACTGGGCACCTACCTTGGTTTTCCTCTGCAGAATT
ATCCCTACTATGGCAAACTCCTGCAGCCCAAATACCTGCAGCCTCTGCTTGTTGTACAGTTCACCAACCTTACCATGGAC
ACTGAAATTCGCCTA

Alignment

ORF - retro_hsap_2924 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.05 %
• Parental protein coverage: 89.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KAKEEGSWKKFIWNSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLTISEFKPTYQDRVA-
          KA.EEGSWKKF.WNSEKKEFLGRTGGSWFKI.LFY.IFYGCL.GIFIG.IQV.LLTISEFKPTYQ.....
Retrocopy KANEEGSWKKFFWNSEKKEFLGRTGGSWFKIILFYIIFYGCLTGIFIGMIQVVLLTISEFKPTYQNHISG

Parental  -PPGLTQIPQIQKTEISFRPNDPKSYEAYVLNIVRFLEKYKDSAQRDDMIFEDCGDVPSEPKERGDFNHE
          .PPGLTQI.QIQ.TEI.F.PNDPK..EAYVLN.VRFLEKYKDSAQ.DDMIFE.C..VPSEPKERGDFN.E
Retrocopy PPPGLTQISQIQQTEIAFHPNDPKHCEAYVLNVVRFLEKYKDSAQKDDMIFENCDNVPSEPKERGDFNQE

Parental  RGER-KVCRFKLEWLGNCSGLNDETYGYKEGKPCIIIKLNRVLGFKPKPPKNESLETYPVMKYNPNVLPV
          .GER.KVCRFKLEWLGNCSGLND.TY.Y.EGKP..IIKL..VLGFKPK.P.NESLETYPVMKYN..V.PV
Retrocopy *GER<KVCRFKLEWLGNCSGLNDKTYSYEEGKPHVIIKLK*VLGFKPKSPENESLETYPVMKYNASVFPV

Parental  QCTGKRDEDKDKVGNVEYFGLGNSPGFPLQYYPYYGKLLQPKYLQPLLAVQFTNLTMDTEIRI
          QCTG..DEDKDK..NVEYFGLG...GFPLQ.YPYYGKLLQPKYLQPLL.VQFTNLTMDTEIR.
Retrocopy QCTG*QDEDKDKNRNVEYFGLGTYLGFPLQNYPYYGKLLQPKYLQPLLVVQFTNLTMDTEIRL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	0.04 RPM	9.52 RPM
bodymap2_adrenal	0.31 RPM	22.21 RPM
bodymap2_brain	0.00 RPM	1093.60 RPM
bodymap2_breast	0.00 RPM	65.18 RPM
bodymap2_colon	0.15 RPM	137.44 RPM
bodymap2_heart	0.06 RPM	238.04 RPM
bodymap2_kidney	0.06 RPM	3075.27 RPM
bodymap2_liver	0.00 RPM	155.32 RPM
bodymap2_lung	0.09 RPM	147.68 RPM
bodymap2_lymph_node	0.00 RPM	27.94 RPM
bodymap2_ovary	0.12 RPM	180.51 RPM
bodymap2_prostate	0.00 RPM	91.35 RPM
bodymap2_skeletal_muscle	0.00 RPM	548.78 RPM
bodymap2_testis	0.00 RPM	156.82 RPM
bodymap2_thyroid	0.00 RPM	644.07 RPM
bodymap2_white_blood_cells	0.02 RPM	6.32 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2924 was not detected

EST

No EST(s) were mapped for retro_hsap_2924 retrocopy.

TSS

No TSS is located nearby retro_hsap_2924 retrocopy 5' end.

Lab

retro_hsap_2924 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2924 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1979
Gorilla gorilla	retro_ggor_2027
Callithrix jacchus	retro_cjac_2288

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010317	1 retrocopy	retro_cjac_2288,
Homo sapiens	ENSG00000069849	2 retrocopies	retro_hsap_1387, retro_hsap_2263,
Homo sapiens	ENSG00000143153	1 retrocopy	retro_hsap_2924 ,
Gorilla gorilla	ENSGGOG00000002499	1 retrocopy	retro_ggor_2027,
Pan troglodytes	ENSPTRG00000001653	1 retrocopy	retro_ptro_1979,
Xiphophorus maculatus	ENSXMAG00000016407	1 retrocopy	retro_xmac_22,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.04 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.11 RPM
CEU_NA12751	0.17 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.08 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.05 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.09 RPM
FIN_HG00328	0.07 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.06 RPM
GBR_HG00099	0.12 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.08 RPM
GBR_HG00119	0.12 RPM
GBR_HG00131	0.11 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.07 RPM
GBR_HG00137	0.05 RPM
GBR_HG00142	0.11 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.07 RPM
TSI_NA20518	0.08 RPM
TSI_NA20532	0.17 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.16 RPM
YRI_NA18870	0.17 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.10 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.14 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.04 RPM

---

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).