RetrogeneDB ID: retro_ggor_1535

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 20:28544965..28546483(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK5RAP3
• Ensembl ID: ENSGGOG00000022994
• Aliases: None
• Description: None

Sequence

>retro_ggor_1535
ATGGAAGACCATCAGCACATGCCCATCGACATCCAGACCAGCAAGCTGCTCGATTGGCTTGTGGACAGAAGGTACTGCAA
CCTGAAATGGCAGAGTCTGGTGCTGACGATCTGAGAGAAGATCAATGCTGCCATCCAGGACATGCCAGAGAGCGAAGAGA
TCACCCAGCTGCTGTCTGGATCCTACATTCACTACTTTCACTGCCTAAGAATCCTGGACCTTTTTAAAGGCACAGAGGCC
TCCACGAAAAATATTTTTGGCTGATACTCTTCACAGTGGATGAAGGATTGGCAGGAGATTATAGCCCTGTATGAGAAGGA
CAACACCTACTTAGTGGAACTCTCTAGCCTCCTTGTTTGGAATGTCAACTATGAGATCCCCTCACTGAAGAAGCAGATTG
CCAAGTGCCAGCAGCTGCAGCAAGAATACAGCTGCAAGGAAGAGGAGTGTCAGGCAGGGGCTGCTGAGATGGGGGAGCAG
TTCTACCACTCCTGCAAGCAGTATGGCATCATGGGCGAAAATACCCGAGGAGAACTTCTGGCCCTGGTGAAGGACCTGCC
AAGTCAGCTGGCTGAGACTGGGGCAGCGGTGCAGCAGTCCCTGGGGGAAGCCATCGACGTGTACCAGGCCTCTGTGGGGT
TTGTGTGTGAGAGCCCCACAGAGCAGTTGTTGCCAATGCTGCAGTTCGTGCAGAAGTGGGGAAACTCAACGGTGTATGAG
TGGAGGACAGGGACAGAGCCCTCTGTGGTGGAGCGACCCCACCTCGAGGAGCTTCCTGAGCAGGTGGCAGAAGACGCGAT
TGACTGGGGCGACTTTGGGGTAGAGGCAGTGTCTGAGGGGACTGACGCTGGCATCTCTGCCGAGGCTGCTGGAATCGACT
GGGGCATCTTCCCGGAATCAGATTCAAAGGACCTTGGAGATGATGGGATAGACTAGGGAGACGATGCTGTTGCTTTGCAG
ATCACAGTGTTGGAAGCAGGAATCCAGGCTCCAGAAGGTGTTGCCAGGGGCCCAGATGCTCTGACACTTCTTGAATACAC
TGAGGCCCAGAATCAGTTCCTTGATGAGCTCATGGAACTTGAGATCTTCTTAGCCCAGAGAGCAGTGGAGTTGAGTGAGA
AGGCAGATGTCCTGTCTGTGAGCCAGTTCCAGCTGGCTCCAGCCATCCTGCAGGGCCAGACCAAAGAGAAGATGGTTATC
ATGGTGTCAGTGTTGGAAGACCTGATTGGCAAACTTACCAGTCTTCAACTGCAACACCTGTTTATGATCCTGGCCTCACC
AAGGTATGTGGACCGAGTGACAGAATTCCTCCAGCAAAAGCTGAAGCAGTCCCAGCTGCTGGCTTTGAAGAAAGAGCTGA
TGGTGCAAAAGCAGCAGGAGGCACTTGAGGAGCAGGCGGCTCTGGAGCCTAAGCTGGACCTGCTGCTGGAGAAGACCAAG
GAGCTGCAGAAGCTGATTGAAGCTGACATCTCCAAGAGGTACAGCAGGCGCCCTGTGAACCTGATGGGAACCTCTCTG

Alignment

ORF - retro_ggor_1535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDHQHVPIDIQTSKLLDWLVDRRHCSLKWQSLVLTIREKINAAIQDMPESEEIAQLLSGSYIHYFHCLR
          MEDHQH.PIDIQTSKLLDWLVDRR.C.LKWQSLVLTI.EKINAAIQDMPESEEI.QLLSGSYIHYFHCLR
Retrocopy MEDHQHMPIDIQTSKLLDWLVDRRYCNLKWQSLVLTI*EKINAAIQDMPESEEITQLLSGSYIHYFHCLR

Parental  ILDLLKGTEASTKNIFGRYSSQRMKDWQEIIALYEKDNTYLVELSSLLVRNVNYEIPSLKKQIAKCQQLQ
          ILDL.KGTEASTKNIFG.YSSQ.MKDWQEIIALYEKDNTYLVELSSLLV.NVNYEIPSLKKQIAKCQQLQ
Retrocopy ILDLFKGTEASTKNIFG*YSSQWMKDWQEIIALYEKDNTYLVELSSLLVWNVNYEIPSLKKQIAKCQQLQ

Parental  QEYSRKEEECQAGAAEMREQFYHSCKQYGITGENVRGELLALVKDLPSQLAEIGAAAQQSLGEAIDVYQA
          QEYS.KEEECQAGAAEM.EQFYHSCKQYGI.GEN.RGELLALVKDLPSQLAE.GAA.QQSLGEAIDVYQA
Retrocopy QEYSCKEEECQAGAAEMGEQFYHSCKQYGIMGENTRGELLALVKDLPSQLAETGAAVQQSLGEAIDVYQA

Parental  SVGFVCESPTEQVLPMLRFVQKRGNSTVYEWRTGTEPSVVERPHLEELPEQVAEDAIDWGDFGVEAVSEG
          SVGFVCESPTEQ.LPML.FVQK.GNSTVYEWRTGTEPSVVERPHLEELPEQVAEDAIDWGDFGVEAVSEG
Retrocopy SVGFVCESPTEQLLPMLQFVQKWGNSTVYEWRTGTEPSVVERPHLEELPEQVAEDAIDWGDFGVEAVSEG

Parental  TDSGISAEAAGIDWGIFPESDSKDPGGDGIDWGDDAVALQITVLEAGTQAPEGVARGPDALTLLEYTETR
          TD.GISAEAAGIDWGIFPESDSKD.G.DGID.GDDAVALQITVLEAG.QAPEGVARGPDALTLLEYTE..
Retrocopy TDAGISAEAAGIDWGIFPESDSKDLGDDGID*GDDAVALQITVLEAGIQAPEGVARGPDALTLLEYTEAQ

Parental  NQFLDELMELEIFLAQRAVELSEEADVLSVSQFQLAPAILQGQTKEKMVTMVSVLEDLIGKLTSLQLQHL
          NQFLDELMELEIFLAQRAVELSE.ADVLSVSQFQLAPAILQGQTKEKMV.MVSVLEDLIGKLTSLQLQHL
Retrocopy NQFLDELMELEIFLAQRAVELSEKADVLSVSQFQLAPAILQGQTKEKMVIMVSVLEDLIGKLTSLQLQHL

Parental  FMILASPRYVDRVTEFLQQKLKQSQLLALKKELMVQKQQEALEEQAALEPKLDLLLEKTKELQKLIEADI
          FMILASPRYVDRVTEFLQQKLKQSQLLALKKELMVQKQQEALEEQAALEPKLDLLLEKTKELQKLIEADI
Retrocopy FMILASPRYVDRVTEFLQQKLKQSQLLALKKELMVQKQQEALEEQAALEPKLDLLLEKTKELQKLIEADI

Parental  SKRYGGRPVNLMGTSL
          SKRY..RPVNLMGTSL
Retrocopy SKRYSRRPVNLMGTSL

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	82.62 RPM
SRP007412_cerebellum	0.08 RPM	146.56 RPM
SRP007412_heart	0.00 RPM	30.08 RPM
SRP007412_kidney	0.12 RPM	125.20 RPM
SRP007412_liver	0.16 RPM	130.12 RPM
SRP007412_testis	0.41 RPM	150.94 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_1535 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1535 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2466
Pan troglodytes	retro_ptro_1425

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000108465	1 retrocopy	retro_hsap_2466,
Gorilla gorilla	ENSGGOG00000022994	1 retrocopy	retro_ggor_1535 ,
Nomascus leucogenys	ENSNLEG00000002109	1 retrocopy	retro_nleu_2448,
Ochotona princeps	ENSOPRG00000004107	2 retrocopies	retro_opri_276, retro_opri_480,
Pongo abelii	ENSPPYG00000008888	1 retrocopy	retro_pabe_1818,
Pan troglodytes	ENSPTRG00000009345	1 retrocopy	retro_ptro_1425,