RetrogeneDB ID: retro_hsap_950

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:6586996..6589373(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000256913
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PKP2
• Ensembl ID: ENSG00000057294
• Aliases: PKP2, ARVD9
• Description: plakophilin 2 [Source:HGNC Symbol;Acc:9024]

Sequence

>retro_hsap_950
GCTGGCTGGGAGCAGCGGCCGCGGCAGCCAGTCAAGAGCCTGCGGATCCAGGAGCAGGTGCAGCAGATCCTCGCCCGGAA
GGGCCGCAGCTCCGTGGGCAACGGAAATCTTCACCGAACCAGCAGTGTTCCTGAGTATGTCTACAACCTACACTTGGTTG
AAAATGATTTTGTTGGAGGCCGTTCCCCTGTTCCTAAAACCTATTACATGCTAAAGGCTGGCACAACTGCCACTTATGAA
GGTCGCTGGGGAAGAGGAACAGCACAGTACAGCTCCCAGAAGTCCGTGGAAGAAAGGTATTTGAGGCATCCTCTGAGGAG
ACTGGAGATTTCTCCTGACAGCAGCCCGGAGAGGGCTCACTACACGCACAGCGATTACCAGTACAGCCAGAGAAGCCAGG
CTGGGCACACCCTGCACCACCAAGAAAGCAGGCGGGCCGCCTTCCTGGTGCCACCGAGATATGATCGTTCTGAGATCGCG
GGGGTCCGCCGTACTGGCACCACAAGCAGGCAGCACCACTTTGACACCACAGGCAGTACCAGCGTGGCTCTGTTAGTGAC
ACCGTTTTTGACAGCATCCCTGCCAACCCGGCCCTGCTCACGTACCCCAGGCCAGGGACCAGCCGCAGCATGGGCAACCT
CTTGGAGAAAGAGAACTACCTGAGGGCAGGGCTCACCGTCGGCCAGGTCAGGCCGCTGGTGCCCCTGCGGCCCCTCACTC
AGAACAGGGCTTCCAGGTCCTCCTGGCACCGGAGCTCCTTCCACAGCACCCGCACACCGAGGAAAGCTGGGCCCAGTGTT
GCCGTGGATTCCAGCGGGAGGAGAGCGCACTTGACCGTCGGCCAGGCAGCGGCAGGGGGAAGTGGGAATCTTCTCACCCA
GAGAAGCACTGACTCCCAGCTGGGGAATGCAGACATGGAGATGACTCTGGAGCGAGCAGGGAGTATGCTCGATGCAGACC
AGATGCCGCCGTCCAGGATTTCTGCCGCAGCCACTTTCATACAGCACGAGTGCTTCCAGAAATCTGAAGCTGGGAAGAGG
GTTAACCAGTTTTGTGGCATCCCCAAGCTTCTGCAGCTCCTAAAAGTTCAGAATGAAGATGTTCAGCGAGCTGTGTGGGG
GGCCTTGAGAAACTTACTATTTGAAGACAATGACAACAAATTGGAGGTGGCTGAACTAAATGGGGTAACTCGGCTGCTCC
AGGTGCTGAAGCAAACCAGAGTCTTGGAGACTAAAAAACAACTAACAGGTTTGCTGTGGAATTTGTCATCTAATGACAAA
CTCAAGAATCTCATGATAACAGAAGCATTGCTTATGCTGACCGAGAATATAATCATCTCCTTTTCTGGATGGCCTGAAGG
AGACTACCCAAAAGCGAATGGTTTGCTCGATTTTGACACAGTCTACAACCCACTGGATGTCTAAGAAACATGAGTGCTGC
TGGCCCTGATAGGAGAAAAGCAATGAGAAGATGTGACCGACTCATTGACTCACTGGTCCATTATGTCAGAGGAACCATTG
CGGATTACCAGCCAGATGACAAGGCCACGGAGAATTGTGTGCACATTCTTCATAACCTCTCCTACCAGCTGGAGGTAGAG
CTCCCAGAGAAATATTCCCAGAATATCTATATTCAAAACCCAAATGTCCAGACTAACAACAAAAGTATTGGATGTTTTGG
CAGTCGAAGCAGGAAACTAAAAGAGCAATACTAGGACATGCCGATGCCAGAGGAAAAGAGCAACCCCAAGGGCGTGGAGT
GGCTGTGACACTCCATTGTGATAAGGATGTATCTGTCCTTGATCGCCAAGAGTGTCCCAAACTACACACAGGAAGCCTCC
TTAGGCGCTCTCCAGAACCTCACAGCCGGAAGTGGACCAATGCCGACATCAGTGGCTCAGACAGTCGTCCAGAAGGAAAA
TGGCCTGCAGCACACCCGAAAGATGGTGCATGTCAGTGACCCAAGTGTGAAAAAGACAGCCAACTTGCTGCTGAGGAATC
TGTCCCAGAATCTTTCTCTGCAGAATAAAATTGCCAAAGAAACTCTCCCCAGTTTGGTCTCCATCATTCCTGATACAGTC
CCGAGTACTGACCTTCTCATTGAAACTACAGCCTCTGCCTGTTACATGTTGAACAACGTAATCCAAAACAGTTACCAGAA
TGCACAGCGCCTTCCGAATACCGGGGGCATCCAGAAAATTATGACCATCAGTGCAGGCGATGCCTATGCCTCCAACAAAG
CAAGTAAAGCTGCTTCCATCCTCCTGTATTCTCTGTAGGCACACACGGAACTCCATCATGCCTACAAGAAGGCTCAGTTT
AAGAAGACAGATTTTGTCAACAGCTGGACTGTCAAAGCCTACCACTCCCTTAAAGAC

Alignment

ORF - retro_hsap_950 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.36 %
• Parental protein coverage: 95.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AGSSGRGGQTVKSLRIQEQVQQTLARKGRSSVGNGNLHRTSSVPEYVYNLHLVENDFVGGRSPVPKTYDM
          AG...R..Q.VKSLRIQEQVQQ.LARKGRSSVGNGNLHRTSSVPEYVYNLHLVENDFVGGRSPVPKTY.M
Retrocopy AGWEQRPRQPVKSLRIQEQVQQILARKGRSSVGNGNLHRTSSVPEYVYNLHLVENDFVGGRSPVPKTYYM

Parental  LKAGTTATYEGRWGRGTAQYSSQKSVEERSLRHPLRRLEISPDSSPERAHYTHSDYQYSQRSQAGHTLHH
          LKAGTTATYEGRWGRGTAQYSSQKSVEER.LRHPLRRLEISPDSSPERAHYTHSDYQYSQRSQAGHTLHH
Retrocopy LKAGTTATYEGRWGRGTAQYSSQKSVEERYLRHPLRRLEISPDSSPERAHYTHSDYQYSQRSQAGHTLHH

Parental  QESRRAALLVPPRYARSEIVGVSRAGTTSRQRHFDT-YHRQYQHGSVSDTVFDSIPANPALLTYPRPGTS
          QESRRAA.LVPPRY.RSEI.GV.R.G.T....H.....HRQYQ.GSVSDTVFDSIPANPALLTYPRPGTS
Retrocopy QESRRAAFLVPPRYDRSEIAGVRRTG-TTSRQHHFD<HHRQYQRGSVSDTVFDSIPANPALLTYPRPGTS

Parental  RSMGNLLEKENYLTAGLTVGQVRPLVPLQPVTQNRASRSSWHQSSFHSTRTLREAGPSVAVDSSGRRAHL
          RSMGNLLEKENYL.AGLTVGQVRPLVPL.P.TQNRASRSSWH.SSFHSTRT.R.AGPSVAVDSSGRRAHL
Retrocopy RSMGNLLEKENYLRAGLTVGQVRPLVPLRPLTQNRASRSSWHRSSFHSTRTPRKAGPSVAVDSSGRRAHL

Parental  TVGQAAAGGSGNLLTERSTFTDSQLGNADMEMTLERAVSMLEADHMLPSRISAAATFIQHECFQKSEARK
          TVGQAAAGGSGNLLT.RST..DSQLGNADMEMTLERA.SML.AD.M.PSRISAAATFIQHECFQKSEA.K
Retrocopy TVGQAAAGGSGNLLTQRST--DSQLGNADMEMTLERAGSMLDADQMPPSRISAAATFIQHECFQKSEAGK

Parental  RVNQLRGILKLLQLLKVQNEDVQRAVCGALRNLVFEDNDNKLEVAELNGVPRLLQVLKQTRDLETKKQIT
          RVNQ..GI.KLLQLLKVQNEDVQRAV.GALRNL.FEDNDNKLEVAELNGV.RLLQVLKQTR.LETKKQ.T
Retrocopy RVNQFCGIPKLLQLLKVQNEDVQRAVWGALRNLLFEDNDNKLEVAELNGVTRLLQVLKQTRVLETKKQLT

Parental  GLLWNLSSNDKLKNLMITEALLTLTENIIIPFSGWPEGDYPKANGLLDFDIFYNV-TGCLRNMSSAGADG
          GLLWNLSSNDKLKNLMITEALL.LTENIII.FSGWPEGDYPKANGLLDFD..YN..TGCLRNMS.AG.D.
Retrocopy GLLWNLSSNDKLKNLMITEALLMLTENIIISFSGWPEGDYPKANGLLDFDTVYNP<TGCLRNMSAAGPDR

Parental  RKAMRRCDGLIDSLVHYVRGTIADYQPDDKATENCVCILHNLSYQLEAELPEKYSQNIYIQNRNIQTDNN
          RKAMRRCD.LIDSLVHYVRGTIADYQPDDKATENCV.ILHNLSYQLE.ELPEKYSQNIYIQN.N.QT.NN
Retrocopy RKAMRRCDRLIDSLVHYVRGTIADYQPDDKATENCVHILHNLSYQLEVELPEKYSQNIYIQNPNVQT-NN

Parental  KSIGCFGSRSRKVKEQYQDVPMPEEKSNPKGVEWLWHSIVIRMYLSLIAKSVRNYTQEASLGALQNLTAG
          KSIGCFGSRSRK.KEQY.D.PMPEEKSNPKGVEWL.HSIVIRMYLSLIAKSV.NYTQEASLGALQNLTAG
Retrocopy KSIGCFGSRSRKLKEQY*DMPMPEEKSNPKGVEWL*HSIVIRMYLSLIAKSVPNYTQEASLGALQNLTAG

Parental  SGPMPTSVAQTVVQKESGLQHTRKMLHVGDPSVKKTAISLLRNLSRNLSLQNEIAKETLPDLVSIIPDTV
          SGPMPTSVAQTVVQKE.GLQHTRKM.HV.DPSVKKTA..LLRNLS.NLSLQN.IAKETLP.LVSIIPDTV
Retrocopy SGPMPTSVAQTVVQKENGLQHTRKMVHVSDPSVKKTANLLLRNLSQNLSLQNKIAKETLPSLVSIIPDTV

Parental  PSTDLLIETTASACYTLNNIIQNSYQNARDLLNTGGIQKIMAISAGDAYASNKASKAASVLLYSLWAHTE
          PSTDLLIETTASACY.LNN.IQNSYQNA..L.NTGGIQKIM.ISAGDAYASNKASKAAS.LLYSL.AHTE
Retrocopy PSTDLLIETTASACYMLNNVIQNSYQNAQRLPNTGGIQKIMTISAGDAYASNKASKAASILLYSL*AHTE

Parental  LHHAYKKAQFKKTDFVNSRTAKAYHSLKD
          LHHAYKKAQFKKTDFVNS.T.KAYHSLKD
Retrocopy LHHAYKKAQFKKTDFVNSWTVKAYHSLKD

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	39.80 RPM
bodymap2_adrenal	0.31 RPM	7.12 RPM
bodymap2_brain	0.21 RPM	5.18 RPM
bodymap2_breast	0.14 RPM	6.15 RPM
bodymap2_colon	0.00 RPM	13.46 RPM
bodymap2_heart	0.02 RPM	651.75 RPM
bodymap2_kidney	0.00 RPM	13.81 RPM
bodymap2_liver	0.00 RPM	29.49 RPM
bodymap2_lung	0.00 RPM	3.48 RPM
bodymap2_lymph_node	0.00 RPM	8.30 RPM
bodymap2_ovary	0.08 RPM	45.90 RPM
bodymap2_prostate	0.21 RPM	9.89 RPM
bodymap2_skeletal_muscle	0.00 RPM	10.28 RPM
bodymap2_testis	0.02 RPM	23.19 RPM
bodymap2_thyroid	0.09 RPM	2.98 RPM
bodymap2_white_blood_cells	0.00 RPM	1.69 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_950 was not detected

EST

No EST(s) were mapped for retro_hsap_950 retrocopy.

TSS

No TSS is located nearby retro_hsap_950 retrocopy 5' end.

Lab

retro_hsap_950 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_950 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_657
Gorilla gorilla	retro_ggor_766

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000057294	1 retrocopy	retro_hsap_950 ,
Gorilla gorilla	ENSGGOG00000002106	1 retrocopy	retro_ggor_766,
Nomascus leucogenys	ENSNLEG00000016650	1 retrocopy	retro_nleu_786,
Pan troglodytes	ENSPTRG00000004820	1 retrocopy	retro_ptro_657,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.15 RPM
CEU_NA11843	0.20 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.11 RPM
CEU_NA12751	0.15 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.14 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.09 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.13 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.05 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.14 RPM
GBR_HG00134	0.07 RPM
GBR_HG00137	0.19 RPM
GBR_HG00142	0.08 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.07 RPM
TSI_NA20518	0.17 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.06 RPM
TSI_NA20765	0.04 RPM
TSI_NA20771	0.14 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.16 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.08 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.10 RPM
YRI_NA19118	0.10 RPM
YRI_NA19213	0.07 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.04 RPM

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Indel association:

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