RetrogeneDB ID: retro_ggor_2217

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:138485063..138485742(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS37A
• Ensembl ID: ENSGGOG00000011650
• Aliases: None
• Description: None

Sequence

>retro_ggor_2217
AATTAACATATATTGCTTCCTCCACAATTTCCTCAGGAAAAACCAGTGATCAGTGTTTTTCCACCAATATGACATCACTT
AATGGATAAACAAGGAGTGTATGTTACTTCTCCATTAGCAAACAATTTTACAATGCACTCAGATCTTGGAAAAATTATTC
AGAGTCTGTTGGATGAGTTTTGGAAGAATCCTCCAGTTTTAGCTCCTACTGCAACAGCATTTCCTTACCTATACAGTAAC
CCAAGTGGGATGCCGCCTTATGCTTCTCAAGGTTTTCCATTTCTTCCTCCATATCCCCCAGAAGAAACAAAGAGGAGTAT
CACTCCTTTATCTGTTGCTAATACTGTTTCTTCTTCAACAACAAGTCATACCACAGCCAAGCCCGTCGCTCCTTCATGTG
GCGTCCTTTCAAATCTGCCATTACCCATTTCCACAACGGATGCTTCAATATTGACAAGGCAAAACGGTTTTGGTTACAAG
ATGCCAGATGTCTCTGATGCATTTCCAGAACTCTCAGAACTAAGCGTGTCACGACTCACAGATATGAATGAACAAGAGGA
GGTATTACTAGAACAGTTTCTGACTTTGTCTCAACTAAAACAAATTATTACTGACAAAGATGACTTAGTAAAAAGTATTG
AGGAACTAGCAAGAAAAAAATATCCTTTTGGAGCCCAGC

Alignment

ORF - retro_ggor_2217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.87 %
• Parental protein coverage: 56.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NINILLPPQFPQEKPVISVYPPIRHHLMDKQGVYVTSPLVNNFTMHSDLGKIIQSLLDEFWKNPPVLAPT
          N..ILLPPQFPQEKPVISV.PPI.HHLMDKQGVYVTSPL.NNFTMHSDLGKIIQSLLDEFWKNPPVLAPT
Retrocopy N*HILLPPQFPQEKPVISVFPPI*HHLMDKQGVYVTSPLANNFTMHSDLGKIIQSLLDEFWKNPPVLAPT

Parental  STAFPYLYSNPSGMSPYASQGFPFLPPYPPQEANRSITSLSVADTVSSSTTSHTTAKPAAPSFGVLSNLP
          .TAFPYLYSNPSGM.PYASQGFPFLPPYPP.E..RSIT.LSVA.TVSSSTTSHTTAKP.APS.GVLSNLP
Retrocopy ATAFPYLYSNPSGMPPYASQGFPFLPPYPPEETKRSITPLSVANTVSSSTTSHTTAKPVAPSCGVLSNLP

Parental  LPIPTMDASIPTSQNGFGYKMPDVPDAFPELSELSVSQLTDMNEQEEVLLEQFLTLPQLKQIITDKDDLV
          LPI.T.DASI.T.QNGFGYKMPDV.DAFPELSELSVS.LTDMNEQEEVLLEQFLTL.QLKQIITDKDDLV
Retrocopy LPISTTDASILTRQNGFGYKMPDVSDAFPELSELSVSRLTDMNEQEEVLLEQFLTLSQLKQIITDKDDLV

Parental  KSIEELAR-KNLLLEPS
          KSIEELAR.KN.LLEPS
Retrocopy KSIEELAR>KNILLEPS

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	12.32 RPM
SRP007412_cerebellum	0.00 RPM	14.50 RPM
SRP007412_heart	0.00 RPM	3.60 RPM
SRP007412_kidney	0.00 RPM	20.16 RPM
SRP007412_liver	0.00 RPM	15.99 RPM
SRP007412_testis	0.00 RPM	28.90 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2217 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2217 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3256
Pan troglodytes	retro_ptro_2202
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,