RetrogeneDB ID: retro_ptro_1928

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:143112025..143112694(-)
• Located in intron of: ENSPTRG00000015462

Retrocopy information

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

Parental gene information

• Parental gene symbol: DTWD1
• Ensembl ID: ENSPTRG00000007058
• Aliases: None
• Description: None

Sequence

>retro_ptro_1928
ATGTCTCTCAATCCACCTATATTTCTCAAACGAAGTGAAGAAAATAATTCAAACTTTGTGGAAACAAAGCAGTCACAAAC
TACTTCCATAGCTTCAGAAGATCCCCTTCAAAACTTATGTTTAGCATCTCAAGAAGTTCTTCAAAAAGCTCAGCAAAGTG
GGAGATCAAAATGTCTCAAATGTGGTGGTTCCAGAATGTTCTACTGCTCTACATGTTACATTCCAGTTGAAAATGTACCT
ATTGAACAGATTCCACTTGTGAAACTTCCATTGAAGATTGACATCATTAAACATCCAAATGAAACAGATGGTAAAAGTAC
TGCTATACATGCAAAACTCTTAGCACCTGAATTTGCAAACATTTACACGTATTCTTGTATTCCAGAATATGAAGAAAAGG
ACCATGAAGTTGCACTTGTTTTTCCTGGACCTCAGTCTATCTCAATAAAAGATATTTCTTTTCATCTGCAAAAAAGGATT
CAAAATAATGTTAGCAGCAAAAATGATGACCCTGACAAGTCATCTTTTAAACGCAAAAGAACTGAAGAACAAGCGTTCTG
TGATTTGAATGACAGCAAGTGCAAAGGCACAACACTGAAAAAAATTATATTTATAGATAGCACCTGGAACCAAACAAACA
AAATATTCACTGATGAGCGACTTCAAGGT

Alignment

ORF - retro_ptro_1928 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.07 %
• Parental protein coverage: 73.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLNPPIFLKRSEENSSKFVETKQSQTTSIASEDPLQNLCLASQEVLQKAQQSGRSKCLKCGGSRMFYCY
          MSLNPPIFLKRSEEN.S.FVETKQSQTTSIASEDPLQNLCLASQEVLQKAQQSGRSKCLKCGGSRMFYC.
Retrocopy MSLNPPIFLKRSEENNSNFVETKQSQTTSIASEDPLQNLCLASQEVLQKAQQSGRSKCLKCGGSRMFYCS

Parental  TCYVPVENVPIEQIPLVKLPLKIDIIKHPNETDGKSTAIHAKLLAPEFVNIYTYPCIPEYEEKDHEVALI
          TCY.PVENVPIEQIPLVKLPLKIDIIKHPNETDGKSTAIHAKLLAPEF.NIYTY.CIPEYEEKDHEVAL.
Retrocopy TCYIPVENVPIEQIPLVKLPLKIDIIKHPNETDGKSTAIHAKLLAPEFANIYTYSCIPEYEEKDHEVALV

Parental  FPGPQSISIKDISFHLQKRIQNNVRGKNDDPDKPSFKRKRTEEQEFCDLNDSKCKGTTLKKIIFIDSTWN
          FPGPQSISIKDISFHLQKRIQNNV..KNDDPDK.SFKRKRTEEQ.FCDLNDSKCKGTTLKKIIFIDSTWN
Retrocopy FPGPQSISIKDISFHLQKRIQNNVSSKNDDPDKSSFKRKRTEEQAFCDLNDSKCKGTTLKKIIFIDSTWN

Parental  QTNKIFTDERLQG
          QTNKIFTDERLQG
Retrocopy QTNKIFTDERLQG

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	0.09 RPM	3.29 RPM
SRP007412_cerebellum	0.11 RPM	5.66 RPM
SRP007412_heart	0.03 RPM	2.91 RPM
SRP007412_kidney	0.18 RPM	6.75 RPM
SRP007412_liver	0.03 RPM	2.82 RPM
SRP007412_testis	0.21 RPM	10.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1928 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1928 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1928 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2846
Gorilla gorilla	retro_ggor_1973
Pongo abelii	retro_pabe_2355

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014926	1 retrocopy	retro_cfam_2081,
Cavia porcellus	ENSCPOG00000003461	2 retrocopies	retro_cpor_1476, retro_cpor_250,
Homo sapiens	ENSG00000104047	1 retrocopy	retro_hsap_2846,
Gorilla gorilla	ENSGGOG00000027921	1 retrocopy	retro_ggor_1973,
Nomascus leucogenys	ENSNLEG00000006167	1 retrocopy	retro_nleu_1598,
Otolemur garnettii	ENSOGAG00000013291	1 retrocopy	retro_ogar_499,
Ochotona princeps	ENSOPRG00000002951	2 retrocopies	retro_opri_136, retro_opri_949,
Pongo abelii	ENSPPYG00000006464	2 retrocopies	retro_pabe_2355, retro_pabe_2356,
Pan troglodytes	ENSPTRG00000007058	1 retrocopy	retro_ptro_1928 ,
Vicugna pacos	ENSVPAG00000008358	2 retrocopies	retro_vpac_509, retro_vpac_530,