RetrogeneDB ID: retro_nleu_2448

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397356.1:2953180..2954114(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK5RAP3
• Ensembl ID: ENSNLEG00000002109
• Aliases: None
• Description: None

Sequence

>retro_nleu_2448
ATGGAGGACCATCAGCACATGCCCATCGACATCCAGACCAGCAAGCTGCTCAATTGGCTGGTGGACAGAAGGCATTGCAG
CCTGAAATGGCAGAGTGTGGTGCTGATGATCCAAGAGAAGATCAATGCTGCCATCCAGGACATGCCAGAGAGCGAAGAGA
TCGCCCAACTGCTGTCTGGGTCCTACATTCACTACTTTCGTTGCCTAAGAATCCTGGACCTTCTCAAAGGCACAGAGGCC
TCCACGAAAAATCTTTTTGGCTGATACTCTTCACAGCGGATGAAGGGTTGGCAGGAGATTATAGCCCTGTATGAGAAGGA
CAACACCTACTTAGTGGAACTCTCTAGCCTCCTGGTTCGGAATGTCAACTATGAGATGCCCTCACTGAAGAAGCAGATTG
CCAAGTGCCAGCAGCTGCAGCAAGAATACAGCCGCAAGGAGGAGGAGTGCCAGACAGGGGCTGCCGAGATGCGGGAGCAG
TTCTACCACTCCTGCAAGCAGTGTGGCATCACGGGCGAAAACGTCTGAGGAGAACTGCTGGCCCTGGTGAAGGACCTGCT
GAGTCAGCTGGCTGAGACTGGGGCAGCGGCTCAGCAGTCCCTGGGGGAAGCCATCGACGTGTACCAGGCCCCTGTGGGGT
TTGTGAGAGCCCCACAGAGCAGATGTTGCCAATGCTGCGGTCGTGCAGAAGCAGGGGAACTCAACGGTCTATAAGTGGAG
GACAGGGACAGAGCCCTCTGTGGTGGAGCGACCCCACCTCAAGGAGCTTCCTGAGCAGGTGGCAGAAGACGCGATTGACT
GGGACGACTTTGGGGTAGAGGCAGTGTCTGAGGGGACTAACTCTGGCATCTCTGCCGAGGCTGCTGGAATCGACTGGGGC
ATCTTTCCGGAATCAGATTCAAAGGACCCTGGAGGTGACTGGGGAGACGATGCT

Alignment

ORF - retro_nleu_2448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.62 %
• Parental protein coverage: 62.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEDHQHVPIDIQTSKLLDWLVDRRHCSLKWQSLVLTIREKINAAIQDMPESEEIAQLLSGSYIHYFHCLR
          MEDHQH.PIDIQTSKLL.WLVDRRHCSLKWQS.VL.I.EKINAAIQDMPESEEIAQLLSGSYIHYF.CLR
Retrocopy MEDHQHMPIDIQTSKLLNWLVDRRHCSLKWQSVVLMIQEKINAAIQDMPESEEIAQLLSGSYIHYFRCLR

Parental  ILDLLKGTEASTKNIFGRYSSQRMKDWQEIIALYEKDNTYLVELSSLLVRNVNYEIPSLKKQIAKCQQLQ
          ILDLLKGTEASTKN.FG.YSSQRMK.WQEIIALYEKDNTYLVELSSLLVRNVNYE.PSLKKQIAKCQQLQ
Retrocopy ILDLLKGTEASTKNLFG*YSSQRMKGWQEIIALYEKDNTYLVELSSLLVRNVNYEMPSLKKQIAKCQQLQ

Parental  QEYSRKEEECQAGAAEMREQFYQSCKQYGITGENVRGELLALVKDLPSQLAEIGAAAQQSLGEAIDVYQA
          QEYSRKEEECQ.GAAEMREQFY.SCKQ.GITGENV.GELLALVKDL.SQLAE.GAAAQQSLGEAIDVYQA
Retrocopy QEYSRKEEECQTGAAEMREQFYHSCKQCGITGENV*GELLALVKDLLSQLAETGAAAQQSLGEAIDVYQA

Parental  SVGFVCESP-TEQVLPMLR-FVQKRGNSTVYEWRTGTEPSVVERPHLEELPEQVAEDAIDWGDFGVQAVS
          .VGFV...P.TEQ.LPMLR..VQK.GNSTVY.WRTGTEPSVVERPHL.ELPEQVAEDAIDW.DFGV.AVS
Retrocopy PVGFV-RAP<TEQMLPMLR<VVQKQGNSTVYKWRTGTEPSVVERPHLKELPEQVAEDAIDWDDFGVEAVS

Parental  EGTDSGISAEAAGIDWGIFPESDSKDPGGDGIDWGDDA
          EGT.SGISAEAAGIDWGIFPESDSKDPGGD...WGDDA
Retrocopy EGTNSGISAEAAGIDWGIFPESDSKDPGGD---WGDDA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2448 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,