RetrogeneDB ID: retro_ggor_2841

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:33168002..33168690(-)
• Located in intron of: ENSGGOG00000010253

Retrocopy information

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

Parental gene information

• Parental gene symbol: DFFB
• Ensembl ID: ENSGGOG00000013452
• Aliases: None
• Description: None

Sequence

>retro_ggor_2841
GTGAGTGACATCGGGTGCTTCCTCAGTGCTTTTCGCCTGCCGCACGCGTGGCTCATCCAGGCCGCCCGGCAGCTACTGTG
TGATGAGCAGGCCCCCGCAGAGGCAGAGACTGCTAGCCGACCTCCTGTACGTCAGCCAGAACGTCACAGCCGACACCCGG
GCTGAGGACCCGCTGTGGTTTGAAGGCTTGGAGTCCCGATTTTGGAATAAGTCTGGCTATCTGAGATACAGCTGTGAGAG
CCGGATCCGGAGTTACCTGAGAGAGGTGAGCTCCTGCTCCTCCATGGTGGGTGCAGGGGCTCAGGAGGAATTCCTGCGGG
TCCTCCGCTCCATGTGCCAGAAGCTCCAGTCTGTGCAGTACGACGGCAGCTATACAACAGAGGAGCCAAGGGTGGCAGCC
GTCTCTGCACACCGGAAGGCTAGTTCTCCTGCCAGGGTCCCTTCGACATTGACGGCTGCTTGTCGAGATACTCCATCAAC
CCCTACAGTAACAGGGAGAGCAGGCTCCTCTTCAGGACCTGGAACCTGGATCACATAGTGGAAACAAAAACGCACCATCA
TTCCTACACTGGTGGAAGCAGTTAAAGAACAAGATGGAAGAGAAGTGGACTGGGAATATTTTTATGGCCTGCTTTCTACC
TCAGAGAACCTAAAATTAGTGTTGTCTGCCATAAGAAAACCACCCACA

Alignment

ORF - retro_ggor_2841 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.69 %
• Parental protein coverage: 63.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VSDIGRFLSAFHEPQVGLIQAAQQLLCDEQAP-QRQRLLADLLHNVSQNIAAETRAEDPPWFEGLESRFQ
          VSDIG.FLSAF..P...LIQAA.QLLCDEQAP.QRQRLLADLL..VSQN..A.TRAEDP.WFEGLESRF.
Retrocopy VSDIGCFLSAFRLPHAWLIQAARQLLCDEQAP>QRQRLLADLLY-VSQNVTADTRAEDPLWFEGLESRFW

Parental  SKSGYLRYSCESRIRSYLREVSSYPSTVGAEAQEEFLRVLGSMCQKLRSMQYNGSY-FDRGAKGGSRLCT
          .KSGYLRYSCESRIRSYLREVSS..S.VGA.AQEEFLRVL.SMCQKL.S.QY.GSY...RGAKGGSRLCT
Retrocopy NKSGYLRYSCESRIRSYLREVSSCSSMVGAGAQEEFLRVLRSMCQKLQSVQYDGSY<YNRGAKGGSRLCT

Parental  PEGWFSCQGPFDMDSCLSRHSINPYSNRESRILFSTWNLDHIIE-KKRTIIPTLVEAIKEQDGREVDWEY
          PEG.FSCQGPFD.D.CLSR.SINPYSNRESR.LF.TWNLDHI.E..KRTIIPTLVEA.KEQDGREVDWEY
Retrocopy PEG*FSCQGPFDIDGCLSRYSINPYSNRESRLLFRTWNLDHIVE>QKRTIIPTLVEAVKEQDGREVDWEY

Parental  FYGLLFTSENLKLVHIVCHKKTT
          FYGLL.TSENLKLV.....K..T
Retrocopy FYGLLSTSENLKLVLSAIRKPPT

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	0.48 RPM	2.16 RPM
SRP007412_cerebellum	0.35 RPM	2.95 RPM
SRP007412_heart	0.13 RPM	0.41 RPM
SRP007412_kidney	0.33 RPM	1.51 RPM
SRP007412_liver	0.11 RPM	2.37 RPM
SRP007412_testis	0.31 RPM	0.83 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_2841 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2841 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4240
Callithrix jacchus	retro_cjac_616

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002834	1 retrocopy	retro_cjac_616,
Homo sapiens	ENSG00000169598	1 retrocopy	retro_hsap_4240,
Gorilla gorilla	ENSGGOG00000013452	1 retrocopy	retro_ggor_2841 ,
Macaca mulatta	ENSMMUG00000015174	1 retrocopy	retro_mmul_1150,
Ornithorhynchus anatinus	ENSOANG00000013652	5 retrocopies	retro_oana_116, retro_oana_117, retro_oana_125, retro_oana_27, retro_oana_91,