RetrogeneDB ID: retro_ggor_1072

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 14:83535234..83535714(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000003406
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DIO1
• Ensembl ID: ENSGGOG00000015406
• Aliases: None
• Description: deiodinase, iodothyronine, type I [Source:HGNC Symbol;Acc:2883]

Sequence

>retro_ggor_1072
GGCGGTCCGGCGCCCAACTCCGAGGTGGTTCTGCCCGACGGCTTCCAGAGCCAGCACATCCTCGACTACGCGCAAGGGAA
CCGCCCGCTGGTTCTCAATTTCGGCAGCTGCACCTGACCACCGTTCATGGCGCGCATGAGCGCCTTCCAGCGCCTGGTCA
CCAAGTACCAGAGTGACGTCGACTTCCTCATCATCTACATCGAGGAAGCGCACCCCTCCGACGGCTGGGTCACCACGGAC
TCTCCCTACGTCATCCCACAGCACCGGAGCCTGGAGGACCGGGTCAGCGCAGCGAGGGTACTGCAGCAAGGTGCACCCGG
CTGCGCTCTGGTCCTCGACACCATGGCCAACTCCAGCAGCTCGGCCTATGGTGCCTACTTCGAGCGTCTCTATGTCATCC
AGAGTGGCACTATTATGTACCAGGGCGGCCGTGGCCCCGACGGCTACCAGGTCTCTGAGCTGCGCACTTGGTTGGAACGC

Alignment

ORF - retro_ggor_1072 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.25 %
• Parental protein coverage: 63.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGLAPNCPVVRLSG-QRCNIWEFMQGNRPLVLNFGSCTUPSFMFKFDQFKRLIEDFSSIADFLVIYIEEA
          GG.APN..VV...G.Q...I....QGNRPLVLNFGSCT.P.FM.....F.RL.....S..DFL.IYIEEA
Retrocopy GGPAPNSEVVLPDGFQSQHILDYAQGNRPLVLNFGSCT*PPFMARMSAFQRLVTKYQSDVDFLIIYIEEA

Parental  HASDGWAFKNN-MDIRNHQNLQDRLQAAHLLLARSPQCPVVVDTMQNQSSQLYAALPERLYVIQEGRILY
          H.SDGW........I..H..L.DR..AA..L....P.C..V.DTM.N.SS..Y.A..ERLYVIQ.G.I.Y
Retrocopy HPSDGWVTTDSPYVIPQHRSLEDRVSAARVLQQGAPGCALVLDTMANSSSSAYGAYFERLYVIQSGTIMY

Parental  KGKSGPWNYNPEEVRAVLEK
          .G..GP..Y...E.R..LE.
Retrocopy QGGRGPDGYQVSELRTWLER

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	0.05 RPM
SRP007412_cerebellum	0.00 RPM	0.04 RPM
SRP007412_heart	0.00 RPM	0.06 RPM
SRP007412_kidney	0.04 RPM	54.14 RPM
SRP007412_liver	1.00 RPM	14.69 RPM
SRP007412_testis	0.00 RPM	0.10 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_1072 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1072 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_65

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000211452	1 retrocopy	retro_hsap_65,
Gorilla gorilla	ENSGGOG00000015406	1 retrocopy	retro_ggor_1072 ,
Microcebus murinus	ENSMICG00000014290	1 retrocopy	retro_mmur_1532,
Tursiops truncatus	ENSTTRG00000009105	1 retrocopy	retro_ttru_1421,