RetrogeneDB ID: retro_ptro_912

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:48970481..48970931(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDLIM1
• Ensembl ID: ENSPTRG00000002783
• Aliases: None
• Description: PDZ and LIM domain 1 [Source:UniProtKB/TrEMBL;Acc:K7CAW2]

Sequence

>retro_ptro_912
GAACATGCTCAGCCTCCAATCAGCCTTGTCATTGACAAAGAATCTGAAGTTTGCAAGATGCTTCAGGAGAAACGGGAGTT
GAATGAGCCCCCAAAACAGTCTGTGTCTTTTCTGGTTTTGCAGAAAATCCTGGAGTCTGAAGAAAAAGAGGATCCCAACA
AGCCCTCAGGATTCAGAAGTGTTAAAGGTCCTGTCACTAAAGTGGCTGCATTGATTGGAAATGCTCAGAAGTTGCCTATG
TGTGACAAATGTGGCCCTGGAATTGTCGGTGTGTTCGTGAAGCTGTGGGACCGTCACCGCCATCCCGAGTGTTACTTGTG
CACTGACTGTTGCACCAACCTGAAACAGAGGGGCCATTTCTTTGTGGAGGATCAAATCTACTGTGAGAAGCATGCCTGGG
AGTGAGTCGCACCACCCGAGGTCTACGAAGTGGTTACCGTGTTCCCCAAG

Alignment

ORF - retro_ptro_912 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.0 %
• Parental protein coverage: 50.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DHAQPPSSLVIDKESEVYKMLQEKQELNEPPKQSTSFLVLQEILESEEKGDPNKPSGFRSVKAPVTKVAA
          .HAQPP.SLVIDKESEV.KMLQEK.ELNEPPKQS.SFLVLQ.ILESEEK.DPNKPSGFRSVK.PVTKVAA
Retrocopy EHAQPPISLVIDKESEVCKMLQEKRELNEPPKQSVSFLVLQKILESEEKEDPNKPSGFRSVKGPVTKVAA

Parental  SIGNAQKLPMCDKCGTGIVGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVTPPE
          .IGNAQKLPMCDKCG.GIVGVFVKL.DRHRHPECY.CTDC.TNLKQ.GHFFVEDQIYCEKHA.E.V.PPE
Retrocopy LIGNAQKLPMCDKCGPGIVGVFVKLWDRHRHPECYLCTDCCTNLKQRGHFFVEDQIYCEKHAWE*VAPPE

Parental  GYEVVTVFPK
          .YEVVTVFPK
Retrocopy VYEVVTVFPK

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	0.02 RPM	2.07 RPM
SRP007412_cerebellum	0.04 RPM	3.55 RPM
SRP007412_heart	0.03 RPM	115.65 RPM
SRP007412_kidney	0.03 RPM	28.14 RPM
SRP007412_liver	0.03 RPM	165.44 RPM
SRP007412_testis	0.00 RPM	8.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_912 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_912 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_912 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011182	1 retrocopy	retro_btau_690,
Canis familiaris	ENSCAFG00000028553	1 retrocopy	retro_cfam_2080,
Dasypus novemcinctus	ENSDNOG00000012381	1 retrocopy	retro_dnov_1119,
Homo sapiens	ENSG00000107438	2 retrocopies	retro_hsap_1815, retro_hsap_2681,
Macaca mulatta	ENSMMUG00000000454	2 retrocopies	retro_mmul_1250, retro_mmul_1419,
Mus musculus	ENSMUSG00000055044	2 retrocopies	retro_mmus_2558, retro_mmus_779,
Nomascus leucogenys	ENSNLEG00000013055	3 retrocopies	retro_nleu_1819, retro_nleu_2767, retro_nleu_2970,
Oryctolagus cuniculus	ENSOCUG00000013643	1 retrocopy	retro_ocun_417,
Pongo abelii	ENSPPYG00000002507	2 retrocopies	retro_pabe_1109, retro_pabe_1485,
Pan troglodytes	ENSPTRG00000002783	1 retrocopy	retro_ptro_912 ,
Tarsius syrichta	ENSTSYG00000000834	2 retrocopies	retro_tsyr_1056, retro_tsyr_1224,
Tursiops truncatus	ENSTTRG00000012118	2 retrocopies	retro_ttru_1777, retro_ttru_976,