RetrogeneDB ID: retro_ggor_1877

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:119868493..119869740(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTOV1
• Ensembl ID: ENSGGOG00000010182
• Aliases: None
• Description: None

Sequence

>retro_ggor_1877
ATGGTCCGTCCGCGCCGGGCCCCGTACCGCTCCGGCGTCGGGGACCCCCTCGGGGGTCACGGCCGCCCCGCGCGGCCCCT
CATAGTGCGCGCTGTCCGCTCGCGCTCCTGGCCAGCCAGCCCCCGAGGCCCGCAGTCTATGCAGATCCGGGCCTGCTCGG
CCCCTCCCGTGGAAGGTGCTCTTGTCTTCGGGGCGCTGGGTCCCATCGGTCCCTCCTCACCTGGGCTCACCCTCGGGGGC
CTGGCCGTGAGCGAGCACCGGCTCAGCAACACGCTGCTGGCCTGGAGCGGCGTCCTCGAGTGACAGGAGAAGCGCAGACC
CTACTGTGACTCCACTGTAAAGTTGAGGCGGACCCTGCCCTGCCAAGCCTACGTGAACCAAGGCGAGAACCTGGAGACCA
ACCAGTGGCAGCAGAAGCTGATCATGCAGCTGATCCCGCAGCAGCTGATGACCACCCTGAGACCCCTGTTCCGCAACTCC
CAGCTGGCACAGTTCCACTTCACTAACCGAGACTGCTGCTTGCGCAGTGGGCTCTGCCGCATCATGGGCAACGGCTTCGC
GGGCTGCACGCTGTTTCCCCACATCTCCCCCTGCGAGATGTGCGTGCGCATGCTCCTGTACTCTTCCAAGAGGAAGATCT
TCATGGGCTTCATCCCCTACGACCAGAGCGGCTTCGTCAGCGCCATCCGGCAGGTCATCACTACCCGCAAGCAAGCAGTG
GGACCTGGTAGTGTCAACTCAGGCCCAGTCCAGATCGTCAACAAAAAGTTCCTGGCGTGGAGAGGCGTCATGGAGTGGCA
GGAACCCAGGCCTGAGGCCAAAAGTCGATCCAAGAGGTGGCTGCCGTCCCACGTCTACGTGAACCAGGGGGAGATCATGA
GGACCGACCAGTGGCCGAGGAAGCTGTAAATGCAGCTCATCCCGCAGCAGCTGCTGACCACCTTGTGCTGCTGTTGCGGA
ACTCGCGCCTGGTGCAGTTCCACTTCACCAAGGACCTGGAGACGCTGAAGAGCCTGTGCCAGATCATGGACAATGGCTTC
GCCGGCTGAGTGCATTTTTCCTACAAAGTGTTGTGCGAGATCCGCGTGCTCATGCTCCTGTACTCCTCTGAGAAGAAAAT
CTTCATCGGCCTCATCCTCCGTGACCAGGGCAACTTCCTCAACGGCATACGGCAAGTCATTGCCAACCAGCAGCAGGTCC
TGCAGTGGAACCTGGAGCAGGAGCAGCAGCAGCAAGGAATGGAGGGT

Alignment

ORF - retro_ggor_1877 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVRPRRAPYRSGAGGPLGGRGRPPRPLVVRAVRSRSWPASPRGPQPQFSHLPPAPLQEGARVFGALGPIG
          MVRPRRAPYRSG.G.PLGG.GRP.RPL.VRAVRSRSWPASPRGPQ........AP..EGA.VFGALGPIG
Retrocopy MVRPRRAPYRSGVGDPLGGHGRPARPLIVRAVRSRSWPASPRGPQSMQIRACSAPPVEGALVFGALGPIG

Parental  PSSPGLTLGGLAVSEHRLSNKLLAWSGVLEWQEKRRPYSDSTAKLKRTLPCQAYVNQGENLETDQWPQKL
          PSSPGLTLGGLAVSEHRLSN.LLAWSGVLE.QEKRRPY.DST.KL.RTLPCQAYVNQGENLET.QW.QKL
Retrocopy PSSPGLTLGGLAVSEHRLSNTLLAWSGVLE*QEKRRPYCDSTVKLRRTLPCQAYVNQGENLETNQWQQKL

Parental  IMQLIPQQLLTTLGPLFRNSQLAQFHFTNRDCDSLKGLCRIMGNGFAGCMLFPHISPCEVRVLMLLYSSK
          IMQLIPQQL.TTL.PLFRNSQLAQFHFTNRDC....GLCRIMGNGFAGC.LFPHISPCE..V.MLLYSSK
Retrocopy IMQLIPQQLMTTLRPLFRNSQLAQFHFTNRDCCLRSGLCRIMGNGFAGCTLFPHISPCEMCVRMLLYSSK

Parental  KKIFMGLIPYDQSGFVSAIRQVITTRKQAVGPGGVNSGPVQIVNNKFLAWSGVMEWQEPRPEPNSRSKRW
          .KIFMG.IPYDQSGFVSAIRQVITTRKQAVGPG.VNSGPVQIVN.KFLAW.GVMEWQEPRPE..SRSKRW
Retrocopy RKIFMGFIPYDQSGFVSAIRQVITTRKQAVGPGSVNSGPVQIVNKKFLAWRGVMEWQEPRPEAKSRSKRW

Parental  LPSHVYVNQGEILRTEQWPRKLYMQLIPQQLLTT-LVPLFRNSRLVQFHFTKDLETLKSLCRIMDNGFAG
          LPSHVYVNQGEI.RT.QWPRKL.MQLIPQQLLTT.LV.L.RNSRLVQFHFTKDLETLKSLC.IMDNGFAG
Retrocopy LPSHVYVNQGEIMRTDQWPRKL*MQLIPQQLLTT<LVLLLRNSRLVQFHFTKDLETLKSLCQIMDNGFAG

Parental  CVHFSYKASCEIRVLMLLYSSEKKIFIGLIPHDQGNFVNGIRRVIANQQQVLQRNLEQEQQQRGMGG
          .VHFSYK..CEIRVLMLLYSSEKKIFIGLI..DQGNF.NGIR.VIANQQQVLQ.NLEQEQQQ.GM.G
Retrocopy *VHFSYKVLCEIRVLMLLYSSEKKIFIGLILRDQGNFLNGIRQVIANQQQVLQWNLEQEQQQQGMEG

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	0.10 RPM	55.67 RPM
SRP007412_cerebellum	0.00 RPM	61.30 RPM
SRP007412_heart	0.00 RPM	21.33 RPM
SRP007412_kidney	0.00 RPM	50.66 RPM
SRP007412_liver	0.00 RPM	31.60 RPM
SRP007412_testis	0.00 RPM	55.53 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_1877 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1877 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2694
Pan troglodytes	retro_ptro_1818
Pongo abelii	retro_pabe_2288
Macaca mulatta	retro_mmul_1426

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003495	1 retrocopy	retro_cfam_289,
Callithrix jacchus	ENSCJAG00000004105	1 retrocopy	retro_cjac_445,
Homo sapiens	ENSG00000104960	1 retrocopy	retro_hsap_2694,
Gorilla gorilla	ENSGGOG00000010182	1 retrocopy	retro_ggor_1877 ,
Macaca mulatta	ENSMMUG00000011618	1 retrocopy	retro_mmul_1426,
Nomascus leucogenys	ENSNLEG00000005374	1 retrocopy	retro_nleu_1191,
Pongo abelii	ENSPPYG00000010265	1 retrocopy	retro_pabe_2288,
Pan troglodytes	ENSPTRG00000011321	1 retrocopy	retro_ptro_1818,