RetrogeneDB ID: retro_ptro_1991

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:60996070..60996842(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPOPL
• Ensembl ID: ENSPTRG00000012504
• Aliases: None
• Description: None

Sequence

>retro_ptro_1991
AAAATCATTAGAAGGGACCATTTGCTTGACGAAGCTGAAGGTCTTTTACCAGATGACGAGCTTACATTATTTTGTGAGAT
GAGTGTGGTACTAGATTCAGTAAACATATAAGGACATACTAATACAAATACTTTGAAGGTGGCTGAGTGTCGACTAGGAG
AAGATTTATGTAATCTCTGTGAAAACACAAGATGTACTGACTGTAGTTTTTTGTGAGAGGACAAGAATTTAAAGCTCATA
AATCTGCTGGTACATCCATCCCCAGTTTTTAATGCCATGTTTGAACATGAAATGGAAGAAAACATAAAGAATCGAGTGGA
AATAAATGATTTAGGCCCTGATGTTTTTAAAGAAATGATGAGATTCATTAACACAGGGAAATAACTAAACCTTGACAAAA
TGGCTGACAACTTGTTGGCAGCTGCAGACAAACATGCACTGGGAACAGCTGAAAGTCATGTGTGAGGAAGCTTTGTGTAG
TAATCCCTCAGTAGAAAATGTTGTTGATACACTTGTCCTTGCAGATTTGCACATTGCAGAACAGTTGAAAGCAAAAGCCA
TAGACATTATTAGTAGGTGCAGTGTACTTCGACAACTTGGGTGTAAACATAAGAAAAACTGGAACAGCAACCAAGCAACC
GACATAATGGAAACATCAAGGTGGAAGTCCATGATTCAGTCTCACTCTTACTTAGCAGCAGAAGCCTTCTAAGCACTAGC
ATCTGCACAGTGTCCACAGTTTGGCATTCCACACACACGGCTAAAACAGTCC

Alignment

ORF - retro_ptro_1991 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.99 %
• Parental protein coverage: 65.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KFIRRDFLLDEANGLLPDDKLTLFCEVSVVQDSVNISGHTNTNTLKVPECRLAEDLGNLWENTRFTDCS-
          K.IRRD.LLDEA.GLLPDD.LTLFCE.SVV.DSVNI.GHTNTNTLKV.ECRL.EDL.NL.ENTR.TDCS.
Retrocopy KIIRRDHLLDEAEGLLPDDELTLFCEMSVVLDSVNI*GHTNTNTLKVAECRLGEDLCNLCENTRCTDCS<

Parental  FFVRGQEFKAHKSVLAARSPVF-NAMFEHEMEESKKNRVEINDLDPEVFKEMMRFIYTGRAPNLDKMADN
          FFVRGQEFKAHKS......P.F.NAMFEHEMEE..KNRVEINDL.P.VFKEMMRFI.TG...NLDKMADN
Retrocopy FFVRGQEFKAHKSA-GTSIPSF>NAMFEHEMEENIKNRVEINDLGPDVFKEMMRFINTGK*LNLDKMADN

Parental  LLAAADKYAL-ERLKVMCEEALCSNLSVENVADTLVLADLHSAEQLKAQAIDFINRCSVLRQLGCKDGKN
          LLAAADK.AL.E.LKVMCEEALCSN.SVENV.DTLVLADLH.AEQLKA.AID.I.RCSVLRQLGCK..KN
Retrocopy LLAAADKHAL>EQLKVMCEEALCSNPSVENVVDTLVLADLHIAEQLKAKAIDIISRCSVLRQLGCKHKKN

Parental  WNSNQATDIMETSGWKSMIQSHPHLVAEAFRALASAQCPQFGIPRKRLKQS
          WNSNQATDIMETS.WKSMIQSH..L.AEAF.ALASAQCPQFGIP..RLKQS
Retrocopy WNSNQATDIMETSRWKSMIQSHSYLAAEAF*ALASAQCPQFGIPHTRLKQS

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	11.51 RPM
SRP007412_cerebellum	0.00 RPM	14.02 RPM
SRP007412_heart	0.00 RPM	16.03 RPM
SRP007412_kidney	0.00 RPM	23.51 RPM
SRP007412_liver	0.03 RPM	9.56 RPM
SRP007412_testis	0.00 RPM	9.91 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1991 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1991 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1991 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014763	1 retrocopy	retro_dnov_546,
Homo sapiens	ENSG00000144228	2 retrocopies	retro_hsap_2943, retro_hsap_3048,
Gorilla gorilla	ENSGGOG00000016285	1 retrocopy	retro_ggor_2040,
Macaca mulatta	ENSMMUG00000002560	2 retrocopies	retro_mmul_1884, retro_mmul_1885,
Nomascus leucogenys	ENSNLEG00000013800	1 retrocopy	retro_nleu_1629,
Oryctolagus cuniculus	ENSOCUG00000006944	1 retrocopy	retro_ocun_1842,
Pongo abelii	ENSPPYG00000012825	4 retrocopies	retro_pabe_2438, retro_pabe_2439, retro_pabe_2440, retro_pabe_2599,
Pan troglodytes	ENSPTRG00000012504	2 retrocopies	retro_ptro_1991 , retro_ptro_2054,