RetrogeneDB ID: retro_ptro_39

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:132336591..132337620(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000040085
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000011126
• Aliases: None
• Description: None

Sequence

>retro_ptro_39
ATGGGGAACGTGTTGGCCGCCAGGTCGCCGCCCGCAGGGCCGCCACCGCCGCCTGCGCCGGCCCTCGTGGAGCTGCCGCC
ACCTCCGCCCTCGCCGCCGGGCTTCACGCTGCCGCCGCTGGGAGGCGGCCTGGGCGCCGGCACCAGTACGAGTCGAGGTT
CGGAACTGACCCCCGGGGCTGCAACTGCCAGCGCCTCAGGGGCCGCCGAGGATGGGGCCTGCGGCTGCCTGCCCAACCCG
GGCACATTCGGGGAGTGCCACCGGAAGTGCAAGGAGCTGTTTCCCATTCAGATGGAGGGTGTCAAGCTCATAGTCAACAA
AGGGTTGAGTAACCATTTCCAGGTGAACCACACAGTAGCCCTCAGCACAATCAGGGAGTCCAACTACCACTTCGGGGTCA
CGTATGTGGGGACAAAGCAGCTGAGTCCCACAGAGGCGTTCCTTGTATTGGTGGGTGACATGGACAACAGCGGCAGTCTC
AACGCTCAGGTCATTCACCAGCTGGGCCCCTGTCTCAGGTCCAAGATGGCCATCCAGACCCAGCAGTCGAAGTTTGTGAA
CTGGCAGGTGGACGGGGAGTATCGGGGCTCTGACTCACAGCAGCCGTCACCCTGGGGAAACCCAGACATCCTCGTGGGTT
CAGGAATCCTCGTAGCCCACTACCTCCAGAGCATCACGCCTTGCCTGGCCCTGGGCAGAGAGCTGGTCTACCACCAGCAG
CCTGGGGAGGAGGGCACTGTCATGTCTCTAGCTGGGAAATACACATTGAACAACTGGTTGGCAACGGTAACGTTGGGCCA
GGCGGGCATGCACGCAACATACTACCACAAAGCCAGTGACCAGCTGCAGGTGGGTGTGGAGTTTGAGGCCAGCACAAGGA
TGCAGAACACCAGCGTCTCCTTCGGGTACCAGCTGGACCTGCCCAAGGCCAAAGGCTCTGTGGATAGCAACTGGATCGTG
TGTGCCACGTTGGAGAAGAAGCTCCCGCCCCTGCCCCTGACACTGGCCCTTGGGGCCTTCCTGAATCAC

Alignment

ORF - retro_ptro_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.5 %
• Parental protein coverage: 76.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNVLAASSPPAGPPPPPAPALVGLPPPPPSPPGFTLPPLGGSLGAGTSTSRGSERTPGAATASASGAAE
          MGNVLAA.SPPAGPPPPPAPALV.LPPPPPSPPGFTLPPLGG.LGAGTSTSRGSE.TPGAATASASGAAE
Retrocopy MGNVLAARSPPAGPPPPPAPALVELPPPPPSPPGFTLPPLGGGLGAGTSTSRGSELTPGAATASASGAAE

Parental  DGACGCLPNPGTFEECHRKCKELFPIQMEGVKLTVNKGLSNHFQVNHTVALSTIGESNYHFGVTYVGTKQ
          DGACGCLPNPGTF.ECHRKCKELFPIQMEGVKL.VNKGLSNHFQVNHTVALSTI.ESNYHFGVTYVGTKQ
Retrocopy DGACGCLPNPGTFGECHRKCKELFPIQMEGVKLIVNKGLSNHFQVNHTVALSTIRESNYHFGVTYVGTKQ

Parental  LSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQTQQSKFVNWQVDGEYRGSDFTAAVTLGNPDV
          LSPTEAF.VLVGDMDNSGSLNAQVIHQLGP.LRSKMAIQTQQSKFVNWQVDGEYRGSD.......GNPD.
Retrocopy LSPTEAFLVLVGDMDNSGSLNAQVIHQLGPCLRSKMAIQTQQSKFVNWQVDGEYRGSDSQQPSPWGNPDI

Parental  LVGSGLQVGVEFEAST
          LVGSG..V.......T
Retrocopy LVGSGILVAHYLQSIT

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	7.56 RPM	20.29 RPM
SRP007412_cerebellum	7.24 RPM	12.08 RPM
SRP007412_heart	2.62 RPM	5.80 RPM
SRP007412_kidney	6.20 RPM	13.21 RPM
SRP007412_liver	6.15 RPM	15.42 RPM
SRP007412_testis	2.32 RPM	3.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_39 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_39 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_39 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2321

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000130204	5 retrocopies	retro_hsap_1300, retro_hsap_1386, retro_hsap_2321, retro_hsap_2537, retro_hsap_3159,
Gorilla gorilla	ENSGGOG00000023033	1 retrocopy	retro_ggor_1356,
Microcebus murinus	ENSMICG00000014041	1 retrocopy	retro_mmur_420,
Myotis lucifugus	ENSMLUG00000028928	1 retrocopy	retro_mluc_697,
Macaca mulatta	ENSMMUG00000014303	1 retrocopy	retro_mmul_1998,
Nomascus leucogenys	ENSNLEG00000001726	2 retrocopies	retro_nleu_2368, retro_nleu_2542,
Oryctolagus cuniculus	ENSOCUG00000023582	1 retrocopy	retro_ocun_1143,
Pongo abelii	ENSPPYG00000025858	1 retrocopy	retro_pabe_174,
Pan troglodytes	ENSPTRG00000011126	1 retrocopy	retro_ptro_39 ,
Ictidomys tridecemlineatus	ENSSTOG00000009019	1 retrocopy	retro_itri_150,
Drosophila melanogaster	FBgn0016041	1 retrocopy	retro_dmel_74,