RetrogeneDB ID: retro_ggor_1973

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:139800197..139800865(-)
• Located in intron of: ENSGGOG00000012306

Retrocopy information

• Ensembl ID: ENSGGOG00000014226
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DTWD1
• Ensembl ID: ENSGGOG00000027921
• Aliases: None
• Description: None

Sequence

>retro_ggor_1973
ATGTCTCTCAATCCACCTATATTTCTCAAACGAAGTGAAGAAAATAATTCAAACTTTGTGGAAACAAAACAGTCACAAAC
TACTTCCATAGCTTCAGAAGATCCCCTTCAAAACTCATGTTTAGCATCTCAAGAAGTTCTTCAAAAAGCTCAGCAAAGTG
GGAGATCAAAATGTCTCAAATGTGGTGGTTCCAGAATGTTCTACTGCTCTACATGTTACGTTCCAGTTGAAAATGTACCT
ATTGAACAGATTCCACTTGTGAAACTTCCATTGAAGATTGACATCATTAAACACCAAATGAAACAGATGGTAAAAGTACT
GCTATACATGCAAAACTCTTAGCACCTGAATTTGCAAACATTTACACGTATTCTTGTATTCCAGAATATGAAGAAAAGGA
CCATGAAGTTGCACTTGTTTTTCCTGGACCTCAGTCTATCTCAATAAAAGATATTTCTTTTCATCTGCAAAAAAGGATTC
AAAATAATGTTAGCAGCAAAAATGATGACCCTGACAAGTCATCTTTTAAACGCAAAAGAACTGAAGAACAAGCATTCTGT
GATTTGAATGACAGCAAGTGCAAAGGCACAACACTGAAAAAAATTATATTTATAGATAGCACCTGGAATCAAACAAACAA
AATATTCACTGATGAGCGACTTCAAGGT

Alignment

ORF - retro_ggor_1973 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.09 %
• Parental protein coverage: 73.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLNPPIFLKRSEENNSKFVETKQSQTTSIASEDPLQNLCLASQEVLQKAQQSGRSKCLKCGGSRMFYCY
          MSLNPPIFLKRSEENNS.FVETKQSQTTSIASEDPLQN.CLASQEVLQKAQQSGRSKCLKCGGSRMFYC.
Retrocopy MSLNPPIFLKRSEENNSNFVETKQSQTTSIASEDPLQNSCLASQEVLQKAQQSGRSKCLKCGGSRMFYCS

Parental  TCYVPVENVPIEQIPLVKLPLKIDIIKH-PNETDGKSTAIHAKLLAPEFVNIYTYPCIPEYEEKDHEVAL
          TCYVPVENVPIEQIPLVKLPLKIDIIKH.PNETDGKSTAIHAKLLAPEF.NIYTY.CIPEYEEKDHEVAL
Retrocopy TCYVPVENVPIEQIPLVKLPLKIDIIKH<PNETDGKSTAIHAKLLAPEFANIYTYSCIPEYEEKDHEVAL

Parental  IFPGPQSISIKDISFHLQKRIQNNVRGKNDDPDKPSFKRKRTEEQEFCDLNDSKCKGTTLKKIIFIDSTW
          .FPGPQSISIKDISFHLQKRIQNNV..KNDDPDK.SFKRKRTEEQ.FCDLNDSKCKGTTLKKIIFIDSTW
Retrocopy VFPGPQSISIKDISFHLQKRIQNNVSSKNDDPDKSSFKRKRTEEQAFCDLNDSKCKGTTLKKIIFIDSTW

Parental  NQTNKIFTDERLQG
          NQTNKIFTDERLQG
Retrocopy NQTNKIFTDERLQG

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	7.00 RPM
SRP007412_cerebellum	0.12 RPM	7.49 RPM
SRP007412_heart	0.00 RPM	0.84 RPM
SRP007412_kidney	0.00 RPM	5.48 RPM
SRP007412_liver	0.08 RPM	6.20 RPM
SRP007412_testis	0.21 RPM	8.70 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1973 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1973 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2846
Pan troglodytes	retro_ptro_1928
Pongo abelii	retro_pabe_2355

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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,