RetrogeneDB ID: retro_ptro_2202

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:155341754..155342758(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: VPS37A
• Ensembl ID: ENSPTRG00000020019
• Aliases: None
• Description: None

Sequence

>retro_ptro_2202
AATTAACATATATTGCTTCCTCCACAATTTCCTCAGGAAAAACCAGTGATCAGTGTTTTTCCACCAATAGGACATCACTT
AATGGATAAAGAAGGAGTGTATGTTACTTCTCCATTAGCAAACAATTTTACAATGCACTCAGATCTTGGAAAAATTATTC
AGAGTCTGTTGGATGAGTTTGGGAAGAATCCTCCAGTTTTAGCTCCTACTGCAACAGCATTTCCTTACCTATACAGTAAC
CCAAGTGGGATGCCGCCTTATGCTTCTCAAGGTTTTCCATTTCTTCCTCCATATCCCCCAGAAGAAACAAAGAGGAGTTA
TCACTTCTTTATCTGTTGCTAATACTGTTTCTTCTTCAACAACAAGTCATACCACAGCCAAGCCCGTCGCTCCTTCATTT
GGCGTCCTTTCAAATCTGCCATTACCCATTTCCACAACAGATGCTTCAATATTGACGAGCCAAAATGGTTTTGGTTACAA
GATGCCAGATGTCTCTGATGCATTTCCAGAACTCTCAGAACTAAGCGTGTCACGACTCACAGATATGAATGAACAAGAGG
AGGTATTACTAGAACAGTTTCTGACTTTGTCTCAACTGAAACAAATTATTACTGACAAAGACGACTTAGTAAAAAGTATT
GAGGAACTAGCAAGAAAAAAATATCCTTTCGGAGCCCAGCTTGGGAGCCAAAAGGCAAACTGTTTTAGATAAGTATGAAT
TACTTAAACAAATGAAGTCTGCTTTCGAAAAGAAGATGCAAAGGCAGTGTGAACTTAGCGAGAGCTGTAGTGCAAGTGCC
CTACAGGCAAGATTGAAAGTAGCTGCACATGAAGCTGGGGAAGAACCTGATAATATTGTGGAAGACTTTGTGGAGGGAAA
AATGGAAATAAATGATTTTCTCAGTAGCTTCATGGAAAAGAGAACAATTTGCCACTGTAGAAGAGCCAAGGAAGAGAAAC
TTCAGCAGGCAATAGCAATGCATAGCCAATTTCATGCTCCACTA

Alignment

ORF - retro_ptro_2202 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.88 %
• Parental protein coverage: 84.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NINILLPPQFPQEKPVISVYPPIRHHLMDKQGVYVTSPLVNNFTMHSDLGKIIQSLLDEFWKNPPVLAPT
          N..ILLPPQFPQEKPVISV.PPI.HHLMDK.GVYVTSPL.NNFTMHSDLGKIIQSLLDEF.KNPPVLAPT
Retrocopy N*HILLPPQFPQEKPVISVFPPIGHHLMDKEGVYVTSPLANNFTMHSDLGKIIQSLLDEFGKNPPVLAPT

Parental  STAFPYLYSNPSGMSPYASQGFPFLPPYPPQEANRS-ITSLSVADTVSSSTTSHTTAKPAAPSFGVLSNL
          .TAFPYLYSNPSGM.PYASQGFPFLPPYPP.E..RS.ITSLSVA.TVSSSTTSHTTAKP.APSFGVLSNL
Retrocopy ATAFPYLYSNPSGMPPYASQGFPFLPPYPPEETKRS>ITSLSVANTVSSSTTSHTTAKPVAPSFGVLSNL

Parental  PLPIPTVDASIPTSQNGFGYKMPDVPDAFPELSELSVSQLTDMNEQEEVLLEQFLTLPQLKQIITDKDDL
          PLPI.T.DASI.TSQNGFGYKMPDV.DAFPELSELSVS.LTDMNEQEEVLLEQFLTL.QLKQIITDKDDL
Retrocopy PLPISTTDASILTSQNGFGYKMPDVSDAFPELSELSVSRLTDMNEQEEVLLEQFLTLSQLKQIITDKDDL

Parental  VKSIEELARK-NLLLEPILEAKRQTVLDKYELLTQMKSTFEKKMQRQHELSESCSASALQARLKVAAHEA
          VKSIEELARK.N.L.EP.L.AKRQTVLDKYELL.QMKS.FEKKMQRQ.ELSESCSASALQARLKVAAHEA
Retrocopy VKSIEELARK>NILSEPSLGAKRQTVLDKYELLKQMKSAFEKKMQRQCELSESCSASALQARLKVAAHEA

Parental  EEESDNIAEDFLEGKMEIDDFLSSFMEKRTICHCRRAKEEKLQQAIAMHSQFHAPL
          .EE.DNI.EDF.EGKMEI.DFLSSFMEKRTICHCRRAKEEKLQQAIAMHSQFHAPL
Retrocopy GEEPDNIVEDFVEGKMEINDFLSSFMEKRTICHCRRAKEEKLQQAIAMHSQFHAPL

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	15.10 RPM
SRP007412_cerebellum	0.00 RPM	18.18 RPM
SRP007412_heart	0.00 RPM	17.05 RPM
SRP007412_kidney	0.00 RPM	17.31 RPM
SRP007412_liver	0.00 RPM	8.64 RPM
SRP007412_testis	0.11 RPM	64.39 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2202 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2202 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2202 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3256
Gorilla gorilla	retro_ggor_2217
Pongo abelii	retro_pabe_2699

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000682	2 retrocopies	retro_chof_1257, retro_chof_2124,
Callithrix jacchus	ENSCJAG00000011769	1 retrocopy	retro_cjac_1790,
Dipodomys ordii	ENSDORG00000014879	9 retrocopies	retro_dord_257, retro_dord_294, retro_dord_542, retro_dord_544, retro_dord_580, retro_dord_598, retro_dord_631, retro_dord_668, retro_dord_751,
Homo sapiens	ENSG00000155975	1 retrocopy	retro_hsap_3256,
Gorilla gorilla	ENSGGOG00000011650	1 retrocopy	retro_ggor_2217,
Nomascus leucogenys	ENSNLEG00000002558	1 retrocopy	retro_nleu_2687,
Pongo abelii	ENSPPYG00000018386	2 retrocopies	retro_pabe_2699, retro_pabe_2821,
Pan troglodytes	ENSPTRG00000020019	1 retrocopy	retro_ptro_2202 ,