RetrogeneDB ID: retro_hsap_4038

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 8:33579820..33580596(-)
• Located in intron of: ENSG00000253642

Retrocopy information

• Ensembl ID: ENSG00000253569
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VENTX
• Ensembl ID: ENSG00000151650
• Aliases: VENTX, HPX42B, NA88A, VENTX2
• Description: VENT homeobox [Source:HGNC Symbol;Acc:13639]

Sequence

>retro_hsap_4038
ATGCGTCCGTCCTCCTCCCCACCTCGTGGCCGGCAGCAGCCCTCCAGCTTTGGCTCCGTGGACTGGCTCTCCCAGAACAG
CTGCTCAGGGCCGACCCACACCCCCAGGCCTGCCGACGTCTCCCCGGGGAGCCACCCTGGCCCGGGCCAGACATCCGGCA
CCCGGGAGCCCCCTCAGGCCGTCAGCATCAAGAAGGCTCGGTCCTCAAATCTGCCTGCGCCGGAGAGGGCCGTGGCTGGG
TTGGGTAAGAAGCCAAACCCCTGGCAGGCCCCCTGTGTAGGCACAGCCTTCACCACCGAGCAGGTCCGCGCCTTGGAGGG
CGTCTTCCAGCACCACCAGGACCTGGGCCCTCTGGAACGGAAAAGGCTGGCAGGGAGATGCAGCTCTCGGACGTCTAGAC
AAAAACCTGGTTTCAAAAACGCCAGATGAAACAGAAACGACAAACGCAGGACTCCCAGCTGAACAGCCCCTTCTCTGTGT
CTCTCCACGCGCCCCCTGCTTTCCACTCACCGTCTTCTGGCCTTGTCAATACCTGCAGCTGCCGTGCCCTTGGGCACCCC
TGCCAGGGCCCCAGGCTCTGATGCTGCCCCCTGGCTCTCTCTGGGGTCTCTGCCAAGTGGAACAAGAGGCCCTGGCCTCT
GCGGGGGTTTCCTGCTATGGGCAGCCTCTGGCGTACCACCGGCCAAGCCCAGGAAGTGGCGTGCGTACGCTGGGACCAGC
TCTGTCCACGGGGCCCTGGGGCCTGAGCGCCCTGCAGGAGACGGGGGGATGCATTT

Alignment

ORF - retro_hsap_4038 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.19 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRLSSSPPRGPQQLSSFGSVDWLSQSSCSGPTHTPRPADFSLGSLPGPGQTSGAREPPQAVSIKEAAGSS
          MR.SSSPPRG.QQ.SSFGSVDWLSQ.SCSGPTHTPRPAD.S.GS.PGPGQTSG.REPPQAVSIK.A..SS
Retrocopy MRPSSSPPRGRQQPSSFGSVDWLSQNSCSGPTHTPRPADVSPGSHPGPGQTSGTREPPQAVSIKKAR-SS

Parental  NLPAPERTMAGLSKEPNTLRAPRVRTAFTMEQVRTLEGVFQHHQYLSPLERKRLA-REMQLSEVQIKTWF
          NLPAPER..AGL.K.PN...AP.V.TAFT.EQVR.LEGVFQHHQ.L.PLERKRLA.REMQLS.V..KTWF
Retrocopy NLPAPERAVAGLGKKPNPWQAPCVGTAFTTEQVRALEGVFQHHQDLGPLERKRLA<REMQLSDV*TKTWF

Parental  QNRRMKHKRQMQDPQLHSPFSGSLHAPPAFYSTSSGLANG-LQLLCPWAPLSGPQALMLPPGSFWGLCQV
          Q.R.MK.KRQ.QD.QL.SPFS.SLHAPPAF.S.SSGL.N..LQL.CPWAPL.GPQALMLPPGS.WGLCQV
Retrocopy QKRQMKQKRQTQDSQLNSPFSVSLHAPPAFHSPSSGLVNT<LQLPCPWAPLPGPQALMLPPGSLWGLCQV

Parental  AQEALASAGASCCGQPLASHPPTPGR--PSLGPALSTGPRGLCAMPQT-GDAF
          .QEALASAG.SC.GQPLA.H.P.PG.....LGPALSTGP.GL.A...T.GDAF
Retrocopy EQEALASAGVSCYGQPLAYHRPSPGSGVRTLGPALSTGPWGLSALQET>GDAF

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	0.00 RPM	0.44 RPM
bodymap2_adrenal	0.00 RPM	0.53 RPM
bodymap2_brain	0.07 RPM	0.28 RPM
bodymap2_breast	0.00 RPM	0.53 RPM
bodymap2_colon	0.00 RPM	0.10 RPM
bodymap2_heart	0.00 RPM	0.59 RPM
bodymap2_kidney	0.00 RPM	0.45 RPM
bodymap2_liver	0.00 RPM	0.15 RPM
bodymap2_lung	0.00 RPM	1.23 RPM
bodymap2_lymph_node	0.00 RPM	0.93 RPM
bodymap2_ovary	0.00 RPM	2.83 RPM
bodymap2_prostate	0.00 RPM	0.40 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.09 RPM
bodymap2_testis	0.06 RPM	0.60 RPM
bodymap2_thyroid	0.00 RPM	0.30 RPM
bodymap2_white_blood_cells	0.00 RPM	8.94 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4038 was not detected

EST

No EST(s) were mapped for retro_hsap_4038 retrocopy.

TSS

No TSS is located nearby retro_hsap_4038 retrocopy 5' end.

Lab

retro_hsap_4038 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4038 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2736
Gorilla gorilla	retro_ggor_2708

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000151650	4 retrocopies	retro_hsap_1027, retro_hsap_2612, retro_hsap_3973, retro_hsap_4038 ,
Gorilla gorilla	ENSGGOG00000003340	3 retrocopies	retro_ggor_1830, retro_ggor_2668, retro_ggor_2708,
Macaca mulatta	ENSMMUG00000000543	2 retrocopies	retro_mmul_1477, retro_mmul_2294,
Nomascus leucogenys	ENSNLEG00000002047	5 retrocopies	retro_nleu_2033, retro_nleu_2054, retro_nleu_635, retro_nleu_664, retro_nleu_905,
Pan troglodytes	ENSPTRG00000003087	4 retrocopies	retro_ptro_1761, retro_ptro_2698, retro_ptro_2736, retro_ptro_702,

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	0.00 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).