RetrogeneDB ID: retro_ggor_2995

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:41517647..41518537(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDCBP
• Ensembl ID: ENSGGOG00000009019
• Aliases: None
• Description: None

Sequence

>retro_ggor_2995
ATGTCTCTCTATCCATCTCTTGAAGACTTGAAGGTAGACAAAGTAATTGGGGCTCAAACTACTTTTTCTACAAACTCTGC
CAATCCAGCAATTCTGTCAGAAGCTTCTGCTCCCATCTCTCAAAATGGAAATCTCTATCCCAAATGATATCCAGAGCTCT
CTCAGTACATGGGCCTGAGTTTAAATGAAGAAGAAATATGTGCAAATGTGGCCATGGTTTCTGGTGCACCAATTCAGGGG
CAGTTGGTAGCAAGACCTTCCAGTATGAACTATATGGTGGCTCCTGTAACTGGTAATAATGTTGGAATTCACAGAGCAGA
AATTAAGCAAGGGATTTGTGAAGTCATTTTGTGTAAGGATCAAGATGGAAAAATTGGACTCAGGCTTAAATCAATAGATA
ATGGTATATTTGTTCAGCTAGTCCAGGCTAATTCTCCAGCCTCATTGGTTGGTCTGCGAATTGAGGACCAAGTACTCCAG
ATTAATAGTGAAAACTGTGCAGGGTAGAGCTCTGATAAAGCGCACAAGGTGCTCAAACAGAATTTTGGAGAGATTACCAT
GACCATTCATGACAGGCCGTTTGAACGGACGATTACCATGCATAAGGATAGCACTGGACATGTTGGTTTTATCTTTAAAA
ATGGAAAAATAACATCCATAGTGAAAGATAGCTCTGCAGCCAGAAATGGTCTTCTCACAGAACATAACATCTGTGAAATC
AATGGACAGAATGTCATTGAATTGAAGGACTCTCAAATTGCAGATATACTGTCAACATCTGGGACTGTAGTTACTATTAC
AATCATGCCGCTTTTATCTTTGAACACATTATTAAGCGGATGGCACCAAGCATTATGAAAAGCCTAATGGACCACACCAT
TTCTGAGGTT

Alignment

ORF - retro_ggor_2995 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLYPSLEDLKVDKVIQAQTAFSANPANPAILSEASAPIPHDGNLYPRLYPELSQYMGLSLNEEEIRANV
          MSLYPSLEDLKVDKVI.AQT.FS.N.ANPAILSEASAPI...GNLYP..YPELSQYMGLSLNEEEI.ANV
Retrocopy MSLYPSLEDLKVDKVIGAQTTFSTNSANPAILSEASAPISQNGNLYPK*YPELSQYMGLSLNEEEICANV

Parental  AVVSGASLQGQLVARPSSINYMVAPVTGNDVGIRRAEIKQGIREVILCKDQDGKIGLRLKSIDNGIFVQL
          A.VSGA..QGQLVARPSS.NYMVAPVTGN.VGI.RAEIKQGI.EVILCKDQDGKIGLRLKSIDNGIFVQL
Retrocopy AMVSGAPIQGQLVARPSSMNYMVAPVTGNNVGIHRAEIKQGICEVILCKDQDGKIGLRLKSIDNGIFVQL

Parental  VQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTITMHKDSTGHVG
          VQANSPASLVGLR..DQVLQIN.ENCAG.SSDKAHKVLKQ.FGE.ITMTI.DRPFERTITMHKDSTGHVG
Retrocopy VQANSPASLVGLRIEDQVLQINSENCAG*SSDKAHKVLKQNFGE-ITMTIHDRPFERTITMHKDSTGHVG

Parental  FIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMP-AFIFEHII
          FIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVI.LKDSQIADILSTSGTVVTITIMP.AFIFEHII
Retrocopy FIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIELKDSQIADILSTSGTVVTITIMP<AFIFEHII

Parental  KRMAPSIMKSLMDHTIPEV
          KRMAPSIMKSLMDHTI.EV
Retrocopy KRMAPSIMKSLMDHTISEV

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	0.05 RPM	64.35 RPM
SRP007412_cerebellum	0.00 RPM	41.09 RPM
SRP007412_heart	0.06 RPM	16.17 RPM
SRP007412_kidney	0.00 RPM	79.73 RPM
SRP007412_liver	0.03 RPM	89.74 RPM
SRP007412_testis	0.00 RPM	58.74 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_2995 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2995 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4810
Pan troglodytes	retro_ptro_3200
Pongo abelii	retro_pabe_3738
Macaca mulatta	retro_mmul_2564

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006161	1 retrocopy	retro_amel_654,
Bos taurus	ENSBTAG00000019910	2 retrocopies	retro_btau_1035, retro_btau_383,
Canis familiaris	ENSCAFG00000007112	1 retrocopy	retro_cfam_112,
Choloepus hoffmanni	ENSCHOG00000003565	5 retrocopies	retro_chof_1063, retro_chof_1151, retro_chof_1910, retro_chof_713, retro_chof_970,
Equus caballus	ENSECAG00000015053	1 retrocopy	retro_ecab_439,
Homo sapiens	ENSG00000137575	2 retrocopies	retro_hsap_3971, retro_hsap_4810,
Gorilla gorilla	ENSGGOG00000009019	2 retrocopies	retro_ggor_2666, retro_ggor_2995 ,
Loxodonta africana	ENSLAFG00000010757	1 retrocopy	retro_lafr_1044,
Microcebus murinus	ENSMICG00000003968	1 retrocopy	retro_mmur_170,
Myotis lucifugus	ENSMLUG00000004807	1 retrocopy	retro_mluc_12,
Macaca mulatta	ENSMMUG00000017296	1 retrocopy	retro_mmul_2564,
Mustela putorius furo	ENSMPUG00000010339	5 retrocopies	retro_mputfur_1055, retro_mputfur_1340, retro_mputfur_292, retro_mputfur_829, retro_mputfur_933,
Nomascus leucogenys	ENSNLEG00000001408	2 retrocopies	retro_nleu_2185, retro_nleu_2525,
Otolemur garnettii	ENSOGAG00000013462	1 retrocopy	retro_ogar_3259,
Procavia capensis	ENSPCAG00000016432	1 retrocopy	retro_pcap_186,
Pongo abelii	ENSPPYG00000018612	3 retrocopies	retro_pabe_3265, retro_pabe_3266, retro_pabe_3738,
Pan troglodytes	ENSPTRG00000020277	2 retrocopies	retro_ptro_2696, retro_ptro_3200,
Tupaia belangeri	ENSTBEG00000013965	1 retrocopy	retro_tbel_2142,