RetrogeneDB ID: retro_ptro_1425

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 20:28016363..28017881(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK5RAP3
• Ensembl ID: ENSPTRG00000009345
• Aliases: None
• Description: None

Sequence

>retro_ptro_1425
ATGGAGGACCATCAGCACATGCCCATCGACATCCAGACCAGCAACCTGCTCGATTGGCTTGTGGACAGAAGGTACTGCAG
CCTGAAATGGCAGAGTCTGATGCTGACGATCTGAGAGAAGATCAGTGCTGCCATCCAGGACATGCCAGAGAGCGAAGTGA
TCGCCCAGCTGCTGTCTGGATCCTACATTCACGACTTTCACTGCCTAAGAATCCTGGACCTTTTCAAAGGCACAGAGGCC
TCCACAAAAAATATTTTTGGCTGATACTCTTCACAGTGGATGAAGGATTGGCAGGAGATTATAGCCCTGTATGAGAAGGA
CAACACCTACTTAGTGGAACTCTCTAGCCTCCTGGTTTGGAATGTCAACTATGAGATCCCCTCACTGAAGAAGCAGATTG
CCAAGTGCCAGCAGCTGCAGCAAGAATACAGCTGCAAGGAGGAGGAGTGCCAGGCAGGGGCTGCTGAGATGGGGGAGCAG
TTCTACCACTCCTGCAAGCAGTATGGCATCATGGGCGAAAATACCCGAGGAGAACTGCTGGCCCTGGTGAAGGACCTGCC
AAGTCAGCTGGCTGAGACTGGGGCAGCGGCGCAGCAGTCCCTGGGGGAAGCCATCGACGTGTACCAGGCCTCTGTGGGGT
TTGTGTGTGAGAGCCCCACAGAGCAGGTGTTGCCAATGCTGCGGTTCGTGCAGAAGTGGGGAAACTCAACAGTGTACGAG
TGGAGGACAGGGACAGAGCCCTCTGTGGTGGAGCGACCCCACCTCGAGGAGCTTCCTGAGCAGGTGGCAGAAGACGCGAT
TGACTGGGGCGACTTTGGGGTAGAGGCAGTTTCTGAGGGGACTGACGCTGGCATCTCTGCCGAGGCTGCTGGAATCGACT
GGGGCATCTTCCCGGAATCAGATTCAAAGGACCTTGGAGATGATGGGATAGACTAGGGAGACGATGCTGTTGCTTTGCAG
ATCACAGTGTTGGAAGCAGGAATCCAGGCTCCAGAAGGTGTTGCCAGGGGCCCAGATGCTCTGACACTTCTTGAATACAC
TGAGACCCAGAATCAGTTCCTTGATGAGCTCATGGAACTTGAGATCTTCTTAGCCCAGAGAGCAGTGGAGTTGAGTGAGA
AGGCAGATGTCCTGTCTGTGAGCCAGTTCCAGCTGGCTCCAGCCATCCTGCAGGGCCAGACCAAAGAGAAGATGGTTATC
ATGGTGTCAGTGTTGGAAGATCTGATTGGCAAACTTACCAGTCTTCAACTGCAACACCTGTTTATGATCCTGGCCTCACC
AAGGTATGTGGACCGAGTGACTGAATTCCTCCAGCAAAACCTGAAGCAGTCCCAGCTGCTGGCTTTGAAGAAAGAGCTGA
TGGTGCAGAAGCAGCAGGAGGCACTTGAGGAGCAGGAGGCTCTGGAGCCTAAGCTGGACCTGCTGCTGGAGAAGACCAAG
GAGCTGCAGAAGCTGATTGAAGCTGACATCTCCAAGAGGTACAGCGGGCGCCCTGTGAACCTGATGGGAACCTCTCTG

Alignment

ORF - retro_ptro_1425 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDHQHVPIDIQTSKLLDWLVDRRHCSLKWQSLVLTIREKINAAIQDMPESEEIAQLLSGSYIHYFHCLR
          MEDHQH.PIDIQTS.LLDWLVDRR.CSLKWQSL.LTI.EKI.AAIQDMPESE.IAQLLSGSYIH.FHCLR
Retrocopy MEDHQHMPIDIQTSNLLDWLVDRRYCSLKWQSLMLTI*EKISAAIQDMPESEVIAQLLSGSYIHDFHCLR

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

Parental  QEYSRKEEECQAGAAEMREQFYHSCKQYGIMGENVRGELLALVKDLPSQLAEIGAAAQQSLGEAIDVYQA
          QEYS.KEEECQAGAAEM.EQFYHSCKQYGIMGEN.RGELLALVKDLPSQLAE.GAAAQQSLGEAIDVYQA
Retrocopy QEYSCKEEECQAGAAEMGEQFYHSCKQYGIMGENTRGELLALVKDLPSQLAETGAAAQQSLGEAIDVYQA

Parental  SVGFVCESPTEQVLPMLRFVQKRGNSTVYEWRTGTEPSVVERPHLEELPEQVAEDAIDWGDFGVEAVSEG
          SVGFVCESPTEQVLPMLRFVQK.GNSTVYEWRTGTEPSVVERPHLEELPEQVAEDAIDWGDFGVEAVSEG
Retrocopy SVGFVCESPTEQVLPMLRFVQKWGNSTVYEWRTGTEPSVVERPHLEELPEQVAEDAIDWGDFGVEAVSEG

Parental  TDSGISAEAAGIDWGIFPESDSKDPGGDGIDWGDDAVALQITVLEAGTQAPEGVARGPDALTLLEYTETR
          TD.GISAEAAGIDWGIFPESDSKD.G.DGID.GDDAVALQITVLEAG.QAPEGVARGPDALTLLEYTET.
Retrocopy TDAGISAEAAGIDWGIFPESDSKDLGDDGID*GDDAVALQITVLEAGIQAPEGVARGPDALTLLEYTETQ

Parental  NQFLDELMELEIFLAQRAVELSEEADVLSVSQFQLAPAILQGQTKEKMVTMVSVLEDLIGKLTSLQLQHL
          NQFLDELMELEIFLAQRAVELSE.ADVLSVSQFQLAPAILQGQTKEKMV.MVSVLEDLIGKLTSLQLQHL
Retrocopy NQFLDELMELEIFLAQRAVELSEKADVLSVSQFQLAPAILQGQTKEKMVIMVSVLEDLIGKLTSLQLQHL

Parental  FMILASPRYVDRVTEFLQQKLKQSQLLALKKELMVQKQQEALEEQAALEPKLDLLLEKTKELQKLIEADI
          FMILASPRYVDRVTEFLQQ.LKQSQLLALKKELMVQKQQEALEEQ.ALEPKLDLLLEKTKELQKLIEADI
Retrocopy FMILASPRYVDRVTEFLQQNLKQSQLLALKKELMVQKQQEALEEQEALEPKLDLLLEKTKELQKLIEADI

Parental  SRRYSGRPVNLMGTSL
          S.RYSGRPVNLMGTSL
Retrocopy SKRYSGRPVNLMGTSL

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	0.21 RPM	74.20 RPM
SRP007412_cerebellum	1.47 RPM	76.97 RPM
SRP007412_heart	0.32 RPM	19.73 RPM
SRP007412_kidney	2.28 RPM	92.16 RPM
SRP007412_liver	1.70 RPM	74.83 RPM
SRP007412_testis	0.95 RPM	144.38 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1425 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1425 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1425 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2466
Gorilla gorilla	retro_ggor_1535

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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 ,