RetrogeneDB ID: retro_pabe_2699

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:156651743..156652743(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS37A
• Ensembl ID: ENSPPYG00000018386
• Aliases: None
• Description: vacuolar protein sorting 37 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:24928]

Sequence

>retro_pabe_2699
AATTAACATATATTGCTTCCTCCACAATTTCCTCAGGAAAAACCAGTGATCAGTGTTTTTCCACCAATACGACATCACTT
AATGGATAAACAAGGAGTGTATGTTACTTCTCCATTAGCAAACAATTTTACAATGCACTCAAATCTTGGAAAAATTATTC
AGTCTGTTGGATGAGTTTTGGAAGAATCCTCCAGTTTTAGCTCCTACTGCAACAGCATTTCCTTACCTATACAGTAACCC
AAGTGGGATGCCTCCTTATGCTTCTCAAGGTTTTCCATTTCTTCCTCCATATCCCCCAGAAGAAGCAAAGAGGAGTATCA
CTTCTTTATCTGTTGCTAATACTGTTTCTTCTTCAGCAACAAGTCATACCACAGCCAAGCCCGTCGCTCCTTCATTTGGC
GTCCTTTCAAATCTGCCGTTATCCATTTCCACAACAGATGCTTCAATATTGACAAGCCAAAATGGTTTTGGTTACAAGAT
GCCAGATGTCTCTGATGCATTTCCAGAACTCTCAGAACTAAGTGTGTCACGACTCACAGATATGAATGAACAAGAGGAGG
TATTACTAGAACAGTTTCTGACTTTGTCTCAACTAAAACAAATTATTACTGACAAAGATGACTTAGTAAAAAGTATTGAG
GAACTAGCAAGAAAAAAATCTCCTTTTGGAGCCCAGCTTGGGAGCCAAAAGGTAAACTGTTTTAGATAAGTATGAATTAC
TTAAACAAATGAAGTCTGCTTTTGAAAAGAAGATGCAAAGGCAGCATGAACTTAGTGAGAGCTGTAGTGCAAGTGCCCTA
CAGGCAAGATTGCAAGTAGCTGCACATGAAACTGGGGAAGAACCTGATAATATTGCGGAAGACTTCGTGGAGGGAAAAAT
GGAAATAAACTATGTTCTCAGTAGCTTCATGGAAAAGAGAACAATTTGCCACTGTAGAAGAGCCAAGGAAGAGAAATTCA
GCAGGCAATAGCAATGCATAGACAATTTCATGCTCCACTA

Alignment

ORF - retro_pabe_2699 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.13 %
• Parental protein coverage: 84.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NINILLPPQFPQEKPVISVYPPIRHHLMDKQGVYVTSPLVNNFTMHSD-LGKIIQSLLDEFWKNPPVLAP
          N..ILLPPQFPQEKPVISV.PPIRHHLMDKQGVYVTSPL.NNFTMHS..L.K...SLLDEFWKNPPVLAP
Retrocopy N*HILLPPQFPQEKPVISVFPPIRHHLMDKQGVYVTSPLANNFTMHSN>LEKLF-SLLDEFWKNPPVLAP

Parental  TSTAFPYLYSNPSGMSPYASQGFPFLPPYPPQEANRSITSLSVADTVSSSTTSHTTAKPAAPSFGVLSNL
          T.TAFPYLYSNPSGM.PYASQGFPFLPPYPP.EA.RSITSLSVA.TVSSS.TSHTTAKP.APSFGVLSNL
Retrocopy TATAFPYLYSNPSGMPPYASQGFPFLPPYPPEEAKRSITSLSVANTVSSSATSHTTAKPVAPSFGVLSNL

Parental  PLPIPTMDASIPTSQNGFGYKMPDVPDAFPELSELSVSQLTDMNEQEEVLLEQFLTLPQLKQIITDKDDL
          PL.I.T.DASI.TSQNGFGYKMPDV.DAFPELSELSVS.LTDMNEQEEVLLEQFLTL.QLKQIITDKDDL
Retrocopy PLSISTTDASILTSQNGFGYKMPDVSDAFPELSELSVSRLTDMNEQEEVLLEQFLTLSQLKQIITDKDDL

Parental  VKSIEELARK-NLLLEPSLEAKRQTVLDKYELLTQMKSTFEKKMQRQHELSESCSASALQARLKVAAHEA
          VKSIEELARK.NLLLEPSL.AKR.TVLDKYELL.QMKS.FEKKMQRQHELSESCSASALQARL.VAAHE.
Retrocopy VKSIEELARK>NLLLEPSLGAKR*TVLDKYELLKQMKSAFEKKMQRQHELSESCSASALQARLQVAAHET

Parental  EEESDNIAEDFLEGKMEIDDFLSSFMEKRTICHCRRAKEEK-LQQAIAMHSQFHAPL
          .EE.DNIAEDF.EGKMEI...LSSFMEKRTICHCRRAKEEK..QQAIAMH.QFHAPL
Retrocopy GEEPDNIAEDFVEGKMEINYVLSSFMEKRTICHCRRAKEEK<IQQAIAMHRQFHAPL

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	4.70 RPM
SRP007412_cerebellum	0.00 RPM	11.67 RPM
SRP007412_heart	0.00 RPM	5.15 RPM
SRP007412_kidney	0.00 RPM	3.85 RPM
SRP007412_liver	0.00 RPM	7.62 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2699 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2699 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2699 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3256
Pan troglodytes	retro_ptro_2202
Gorilla gorilla	retro_ggor_2217

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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,