RetrogeneDB ID: retro_ggor_1649

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2a:101012947..101013823(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRLF3
• Ensembl ID: ENSGGOG00000005002
• Aliases: None
• Description: None

Sequence

>retro_ggor_1649
GAGATCAAAGAGAGTGCATCACAGACAAGCGATGTTCTCAAACAACATTTTCATGATTTAAAGGGAACCCATGGGAAGCT
CCTGGATGAGCGATTGGTGACCCTTTTGCAAGAGGTTGGCACCACTAAACAGACCATTAAACCACTAGATGATTGCCAGA
AGCTCATAGAACACGGAGTTAACATTCCAGAGGGCTTAGTCCAAGAAGGTGAGATTGCCATGCTTGGTGGTGTAGAAGAG
AATGAGAAACTGTGGAGCTTTACCAAAAAGGCCTTGCACCTTCAGTTGGACAGCATACCAGAAGTACCTTTACTGGTTGA
TGTGCCTTGTTTATCTGCTCAGTTGGATGAGTCTATTCTTAACATCATGAAAGACCACATTCTTAAGCATGGAACAGTAG
CATCTCGCCCACCAGTACAGATAGAAGAACTGATAGAGAAACCTGGAGGCATCATAGTACAATGGTGTAAGGTGGATGAT
GACTTTACGGCACAAGGTGACAGTCTCCAGTTTCGTAAATGTACTTCAAATCATTTTGAGGATGTATATGTAGGTTCCGA
AACTGAATTCAGAGTATTGCACATAGACTCCAACGTTGAAGATCATTTCAGAATCTGCACCCGAAGAGATGGCTGACAGG
AGCAGAGTCCTTGGAGTGTCCCCCAGATAGTTCTTTCCATATTGGAGCCTCATGAGTGGACAGCTGGTTTTGAGAGGAGC
AGTGTGAGCAATGGAAGAAATACGTCATGCCGGAACGATTCTAAATCTTCAGGTGTTCTCAACTCCAGAGCTCCAACTCA
TCTTTCTGGGCAGACATTAATATTTAGAGTTGAAACTGTGGAACTACCAGACAGAAGAGACTGTATAGGAGTGTGC

Alignment

ORF - retro_ggor_1649 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.08 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QIKESASQTRDVLKQHFNDLKGTLGKLLDERLVTLLQEVDTIEQETIKPLDDCQKLIEHGVNTAEDLVRE
          .IKESASQT.DVLKQHF.DLKGT.GKLLDERLVTLLQEV.T..Q.TIKPLDDCQKLIEHGVN..E.LV.E
Retrocopy EIKESASQTSDVLKQHFHDLKGTHGKLLDERLVTLLQEVGTTKQ-TIKPLDDCQKLIEHGVNIPEGLVQE

Parental  GEIAMLGGVGEENEKLWSFTKKASHIQLDSLPEVPLLVDVPCLSAQLDDSILNIVKDHIFKHGTVASRPP
          GEIAMLGGV.EENEKLWSFTKKA.H.QLDS.PEVPLLVDVPCLSAQLD.SILNI.KDHI.KHGTVASRPP
Retrocopy GEIAMLGGV-EENEKLWSFTKKALHLQLDSIPEVPLLVDVPCLSAQLDESILNIMKDHILKHGTVASRPP

Parental  VQIEELIEKPGGIIVRWCKVDDDFTAQDYRLQFRKCTSNHFEDVYVGSETEFIVLHIDPNVDYQFRVCAR
          VQIEELIEKPGGIIV.WCKVDDDFTAQ...LQFRKCTSNHFEDVYVGSETEF.VLHID.NV...FR.C.R
Retrocopy VQIEELIEKPGGIIVQWCKVDDDFTAQGDSLQFRKCTSNHFEDVYVGSETEFRVLHIDSNVEDHFRICTR

Parental  GDGRQEWSPWSVPQIGHSTLVPHEKEWTAGFEGYSLSSRRNIALRNDSESSGVLYSRAPTYFCGQTLTFR
          .DG.QE.SPWSVPQI..S.L.PH..EWTAGFE..S.S..RN...RNDS.SSGVL.SRAPT...GQTL.FR
Retrocopy RDG*QEQSPWSVPQIVLSILEPH--EWTAGFERSSVSNGRNTSCRNDSKSSGVLNSRAPTHLSGQTLIFR

Parental  VETVGQPDRRDSIGVC
          VETV..PDRRD.IGVC
Retrocopy VETVELPDRRDCIGVC

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	10.17 RPM
SRP007412_cerebellum	0.00 RPM	17.14 RPM
SRP007412_heart	0.00 RPM	2.13 RPM
SRP007412_kidney	0.00 RPM	7.40 RPM
SRP007412_liver	0.00 RPM	6.20 RPM
SRP007412_testis	0.00 RPM	16.78 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_1649 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1649 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2133
Pan troglodytes	retro_ptro_1560
Pongo abelii	retro_pabe_1925
Macaca mulatta	retro_mmul_1002

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014163	1 retrocopy	retro_cjac_1183,
Homo sapiens	ENSG00000176390	3 retrocopies	retro_hsap_2121, retro_hsap_2133, retro_hsap_3360,
Gorilla gorilla	ENSGGOG00000005002	3 retrocopies	retro_ggor_1644, retro_ggor_1649 , retro_ggor_2278,
Macaca mulatta	ENSMMUG00000009069	2 retrocopies	retro_mmul_1002, retro_mmul_998,
Mus musculus	ENSMUSG00000017561	1 retrocopy	retro_mmus_368,
Nomascus leucogenys	ENSNLEG00000005850	4 retrocopies	retro_nleu_1957, retro_nleu_2534, retro_nleu_2899, retro_nleu_2900,
Pongo abelii	ENSPPYG00000008142	3 retrocopies	retro_pabe_1925, retro_pabe_1984, retro_pabe_2672,
Pan troglodytes	ENSPTRG00000008963	2 retrocopies	retro_ptro_1560, retro_ptro_2175,