RetrogeneDB ID: retro_hsap_4022

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 8:15546421..15547069(-)
• Located in intron of: ENSG00000104723

Retrocopy information

• Ensembl ID: ENSG00000248423
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CLTA
• Ensembl ID: ENSG00000122705
• Aliases: CLTA, LCA
• Description: clathrin, light chain A [Source:HGNC Symbol;Acc:2090]

Sequence

>retro_hsap_4022
ATGGCTGAGCAACATCCCTTCGGTGTCCCTGCTGGCACCCCTGGGGATCCTGTCCTGGGGAACGGAGTGGCTGGCGCCAG
TGAAGAAGACCCAGCTGCGGCCTTCTTGGCACTGCAAGAGAGCAAGACTATGGGTATCAAGAACAACAAGGTCGCCTTCG
ACATCCTGGATGGTGTCACCCCCAGGCCCCAGCCACAAGGTGAACAGCTGGGAGTCCAGATGCTGTTGACGGAGTGATGA
TGGTGACTACTACCAGGAAAGTAATGGTCCAAGAGACAATTATGCAGCTATTTCACAAGTGGATCGATTCCCATCCAGCC
TGAAAATATATGCAGATGCAAAGAAGAGAAAATGGAATGCTTAGCAGCCCTTGCTGCTTATTCTCCGAAGCAAGAAGCAG
AGTGGAAAGAAAAAGCGATAAATGAGCTAGAAGAATGGCGTGCAAGACAAGACGAGCAGCTACAGAAAAGAAAGGCAAAC
TACAGGGCAGAAGATTTTGTAAATGACATTGACGAGTCATCCCCCTGCACTGGGTGGTAACAGGTGGCCCGGTTGTTTGA
CTGTAACCCCAAGTCAGCAAGCAGGGCAAAGAGGTCTCCTGTATGCACTCAGTCCTCAACTCCCTCAAGCAGGCGACCCC
TGGTGCAC

Alignment

ORF - retro_hsap_4022 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAELDPFGAPAGAPGGPALGNGVAGAGEEDPAAAFLAQQESEIAGIENDE-AFAILDGGAPGPQPHGEP-
          MAE..PFG.PAG.PG.P.LGNGVAGA.EEDPAAAFLA.QES...GI.N...AF.ILDG..P.PQP.GE..
Retrocopy MAEQHPFGVPAGTPGDPVLGNGVAGASEEDPAAAFLALQESKTMGIKNNKVAFDILDGVTPRPQPQGEQ<

Parental  PGGPDAVDGVM-NGEYYQESNGPTDSYAAISQVDRLQS-EPESIRKWREEQMERLEALDANSRKQEAEWK
          .G.PDAVDGVM..G.YYQESNGP.D.YAAISQVDR..S..PE.I....EE.ME.L.AL.A.S.KQEAEWK
Retrocopy AGSPDAVDGVM<DGDYYQESNGPRDNYAAISQVDRFPS<QPENICRCKEEKMECLAALAAYSPKQEAEWK

Parental  EKAIKELEEWYARQDEQLQKTKANNRAAEEAFVNDIDESSPGTEWERVARLCDFNPKS-SKQAKDVSRMR
          EKAI.ELEEW.ARQDEQLQK.KAN.RA..E.FVNDIDESSP.T.W..VARL.D.NPKS.SKQ.K.VS.M.
Retrocopy EKAINELEEWRARQDEQLQKRKANYRA--EDFVNDIDESSPCTGW*QVARLFDCNPKS<SKQGKEVSCMH

Parental  SVLISLKQA-PLVH
          SVL.SLKQA.PLVH
Retrocopy SVLNSLKQA>PLVH

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	76.25 RPM
bodymap2_adrenal	0.00 RPM	93.07 RPM
bodymap2_brain	0.00 RPM	97.00 RPM
bodymap2_breast	0.00 RPM	74.98 RPM
bodymap2_colon	0.00 RPM	93.88 RPM
bodymap2_heart	0.09 RPM	19.86 RPM
bodymap2_kidney	0.08 RPM	91.26 RPM
bodymap2_liver	0.00 RPM	46.15 RPM
bodymap2_lung	0.00 RPM	69.57 RPM
bodymap2_lymph_node	0.00 RPM	69.33 RPM
bodymap2_ovary	0.02 RPM	113.31 RPM
bodymap2_prostate	0.03 RPM	101.79 RPM
bodymap2_skeletal_muscle	0.00 RPM	26.39 RPM
bodymap2_testis	0.00 RPM	98.19 RPM
bodymap2_thyroid	0.00 RPM	104.17 RPM
bodymap2_white_blood_cells	0.00 RPM	68.22 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4022 was not detected

EST

No EST(s) were mapped for retro_hsap_4022 retrocopy.

TSS

No TSS is located nearby retro_hsap_4022 retrocopy 5' end.

Lab

retro_hsap_4022 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4022 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2727

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001137	1 retrocopy	retro_btau_327,
Homo sapiens	ENSG00000122705	2 retrocopies	retro_hsap_4022 , retro_hsap_955,
Macropus eugenii	ENSMEUG00000010858	1 retrocopy	retro_meug_480,
Macaca mulatta	ENSMMUG00000006132	2 retrocopies	retro_mmul_2319, retro_mmul_785,
Monodelphis domestica	ENSMODG00000002610	1 retrocopy	retro_mdom_1148,
Nomascus leucogenys	ENSNLEG00000003874	1 retrocopy	retro_nleu_659,
Pongo abelii	ENSPPYG00000019069	1 retrocopy	retro_pabe_3300,
Pan troglodytes	ENSPTRG00000020930	1 retrocopy	retro_ptro_2727,

Population studies

Expression level across human populations :

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

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Indel association:

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