RetrogeneDB ID: retro_ptro_1560

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:103827920..103828796(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRLF3
• Ensembl ID: ENSPTRG00000008963
• Aliases: None
• Description: None

Sequence

>retro_ptro_1560
GAGATCAAAGAGAGTGCATCACAGACAAGCGATGTTCTCAAACAGCATTTTCATGATTTAAAGGGATCCCATGGGAAGCT
CCTGGATGAGCGATTGGTGACCCTTTTGCAAGAGGTTGGCACCATTAAACAGACCATTAAACCACTAGATGATTGCCAGA
AGCTCATAGAACACAGAGTTAACACTCCAGAGGGCTTAGTCCAAGAAGGTGAGATTGCCATGCTTGGTGGTGTAGAAGAG
AATGAGAAACTGTGGAGCTTTACCAAAAAGGCCTTGCACGTTCAGTTGGACAGCATACCAGAAGTACCTTTACTGGTTGA
TGTGCCTTGTTTATCTGCTCAGCTGGATGAGTCTATTCTTAACATCATGAAAGACCACATTCTTAAGCATGGAACAGTAG
CATCTCGCCCACCAGTACAGATAGAAGAACTGATAGAGAAACCTGGAGGCATCATAGTACAATGGTGTAAGGTGGATGAT
GACTTTACGGCACAAGGTGACAGGCTCCAGTTTCGTAAATGTACTTCAAATCATTTTGAGGATGTATATGTAGGTTCCGA
AACTGAATTCAGAGTATTGCACATAGACTCCAACGTTGAAGATCATTTCAGAATCTGCACCCGAAGAGATGGCTGACAGG
AGCAGAGTCCTTGGAGTGTCCCCCAGATAGTTCATTCCATATTGGAGCCTCATGAGTGGACAGCTGGTTTTGAGAGGAGC
AGTGTGAGCAATGGAAGAAATACGTTATGCCGGAACGATTCTAAATCTTCAGGTGTTCTCAACTCCAGAGCTCCAACTTA
TCTTTCTGGGCAGACATTAATATTTAGAGTTGAAACTGTGGAACTACCAGACAGAAGAGACTGTATAGGAGTGTGC

Alignment

ORF - retro_ptro_1560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.65 %
• Parental protein coverage: 66.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QIKESASQTRDVLKQHFNDLKGTLGKLLDERLVTLLQEVDTIEQETIKPLDDCQKLIEHGVNTAEDLVRE
          .IKESASQT.DVLKQHF.DLKG..GKLLDERLVTLLQEV.TI.Q.TIKPLDDCQKLIEH.VNT.E.LV.E
Retrocopy EIKESASQTSDVLKQHFHDLKGSHGKLLDERLVTLLQEVGTIKQ-TIKPLDDCQKLIEHRVNTPEGLVQE

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

Parental  VQIEELIEKPGGIIVRWCKVDDDFTAQDYRLQFRKCTSNHFEDVYVGSETEFIVLHIDPNVDYQFRVCAR
          VQIEELIEKPGGIIV.WCKVDDDFTAQ..RLQFRKCTSNHFEDVYVGSETEF.VLHID.NV...FR.C.R
Retrocopy VQIEELIEKPGGIIVQWCKVDDDFTAQGDRLQFRKCTSNHFEDVYVGSETEFRVLHIDSNVEDHFRICTR

Parental  GDGRQEWSPWSVPQIGHSTLVPHEWTAGFEGYSLSSRRNIALRNDSESSGVLYSRAPTYFCGQTLTFRVE
          .DG.QE.SPWSVPQI.HS.L.PHEWTAGFE..S.S..RN...RNDS.SSGVL.SRAPTY..GQTL.FRVE
Retrocopy RDG*QEQSPWSVPQIVHSILEPHEWTAGFERSSVSNGRNTLCRNDSKSSGVLNSRAPTYLSGQTLIFRVE

Parental  TVGQPDRRDSIGVC
          TV..PDRRD.IGVC
Retrocopy TVELPDRRDCIGVC

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	18.59 RPM
SRP007412_cerebellum	0.00 RPM	25.09 RPM
SRP007412_heart	0.00 RPM	5.33 RPM
SRP007412_kidney	0.00 RPM	6.77 RPM
SRP007412_liver	0.00 RPM	4.62 RPM
SRP007412_testis	0.00 RPM	25.50 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1560 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1560 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1560 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2133
Gorilla gorilla	retro_ggor_1649
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,