RetrogeneDB ID: retro_ptro_1640

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:130755864..130756482(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSBP4
• Ensembl ID: ENSPTRG00000010709
• Aliases: None
• Description: single stranded DNA binding protein 4 [Source:HGNC Symbol;Acc:15676]

Sequence

>retro_ptro_1640
CCGCACGCACAGCCTGCACCTCATAATCCTAGCAGCATGATGGGACCCCACAGTCAGCCTTTTTTGTCACCGCGATACGC
AGGCGGCCCCAGGCCCCCCGATCAGAATGGGAAACCAGCCTCCGGGAGGAGTTCCTGGGACACAGCCATTGCTGCCCAAT
TCCATGGATCCCGCACGACAACAAGGCCACCCCCACATGGGAGGATCAATGCAGAGAATGAACCCTCCCCGAGGCATGGG
GCCCACGGGTCCCAGCCCACAGAATTACGGCAGCGGCATGAGACCACCACGCAATTCCCTCGGCCCCCCACGCCCGGGAT
TAACATGGGCCCGGGAGCCGGCAGACCCTGGCCCAATCCTAACAGTGCTAACTCAATTCCATACTCCTCCTCATCACCTG
GTACCTATGTGGGACTCCCTGGTGGTGGCGGCCCTCCAGGAACACCCACTATGCCCAGTCCCTCAGATTCAACAAATTCC
AGCGACATCTACACAATGATTAATCCGGTGCCGCCTGGAGGCAGCCGGTCCAACTTCCCGATGGGTCCCGGCTCGGACGG
TCGGATGGGCAGCATGGGCGGCATGGAGCCACACCACATGAACGGATTGTTAGGGTCA

Alignment

ORF - retro_ptro_1640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.74 %
• Parental protein coverage: 64.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PGSQPSPHNPNAPMMGPHGQPFMSPRFPGGPRPT-LRMPSQPPAGLPGSQPLLPGAMEPSPRAQGHPSMG
          P..QP.PHNP...MMGPH.QPF.SPR..GGPRP...RM..QPP.G.PG.QPLLP..M.P..R.QGHP.MG
Retrocopy PHAQPAPHNPSS-MMGPHSQPFLSPRYAGGPRPP>IRMGNQPPGGVPGTQPLLPNSMDPA-RQQGHPHMG

Parental  GPMQRVTPPRGMASVGP--QSYGGGMRPPPNSLAGPGLPAM-NMGPGVRGPWASP-SGNSIPYSSSSPGS
          G.MQR..PPRGM...GP..Q.YG.GMRP.P....GP..P...NMGPG...PW..P.S.NSIPYSSSSPG.
Retrocopy GSMQRMNPPRGMGPTGPSPQNYGSGMRP-PRNSLGPPRPGL<NMGPGAGRPWPNPNSANSIPYSSSSPGT

Parental  YTGPPGGGGPPGTPIMPSPGDSTNSSENMYTIMNPIGQGAGRANFPLGPGPEGPMAAMSAMEPHHVNGSL
          Y.G.PGGGGPPGTP.MPSP.DSTNSS...YT..NP...G..R.NFP.GPG..G.M..M..MEPHH.NG.L
Retrocopy YVGLPGGGGPPGTPTMPSPSDSTNSSD-IYTMINPVPPGGSRSNFPMGPGSDGRMGSMGGMEPHHMNGLL

Parental  YS
          .S
Retrocopy GS

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	0.18 RPM	41.04 RPM
SRP007412_cerebellum	0.00 RPM	10.75 RPM
SRP007412_heart	0.00 RPM	1.57 RPM
SRP007412_kidney	0.03 RPM	7.64 RPM
SRP007412_liver	0.00 RPM	9.82 RPM
SRP007412_testis	0.00 RPM	1.26 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1640 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1640 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1640 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000130511	1 retrocopy	retro_hsap_1911,
Gorilla gorilla	ENSGGOG00000016931	1 retrocopy	retro_ggor_1759,
Pan troglodytes	ENSPTRG00000000770	2 retrocopies	retro_ptro_2618, retro_ptro_2931,
Pan troglodytes	ENSPTRG00000010709	2 retrocopies	retro_ptro_1250, retro_ptro_1640 ,