RetrogeneDB ID: retro_nleu_2441

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397355.1:5745082..5745555(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDKL3
• Ensembl ID: ENSNLEG00000026729
• Aliases: None
• Description: Serine/threonine-protein phosphatase [Source:UniProtKB/TrEMBL;Acc:G1R9F7]

Sequence

>retro_nleu_2441
CATCTTCCTCTCACTGCCTTGGTGGATGGGCAGCTCTTCTGTCTCCATGGTGGCCTGTCGCCATCTGTAGATACACTGCA
TCACATCAGAACACTGAACTGCCTACAGAAAATTCCCCATGAGGGTCCAATGGGTGACTTGCTATACTCAGATCCAGATG
ACCATGGTGGCTGGGGTATATCTCTTTGAGGAGATGGTTACACCTTTGGGCAAGATACTTCTGAGACATTTAATCATGCC
AATGGCCTCAGGTTGGCGTTTAGAGCTCACCAGCTGGTGATGGTGGGACATAACTGGTGTCATGACTAGAATATGGTAGC
CATCTTCAGTACTCCAAACTATTGCTATCATTGTGGTAATCACGCTGCAATCATGGAACTTGATAATGCTCTAAAATACT
CTGTTTGCAGTTTGACCCAGCACCTCACAGAGGCAAGCCACATGTTACTCATTGTACCCCAGATTACTTCCTG

Alignment

ORF - retro_nleu_2441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.99 %
• Parental protein coverage: 51.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFG
          .LPLTALVDGQ.FCLHGGLSPS.DTL.HIR.L..LQ..PHEGPM.DLL.SDPDD.GGWGIS..G.GYTFG
Retrocopy HLPLTALVDGQLFCLHGGLSPSVDTLHHIRTLNCLQKIPHEGPMGDLLYSDPDDHGGWGISL*GDGYTFG

Parental  QDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYSF-LQFD
          QD.SETFNHANGL.L..RAHQLVM.G.NWCHD.N.V.IFS.PNYCY.CGN.AAIMELD..LKYS..LQFD
Retrocopy QDTSETFNHANGLRLAFRAHQLVMVGHNWCHD*NMVAIFSTPNYCYHCGNHAAIMELDNALKYSV<LQFD

Parental  PAPRRGEPHVTRRTPDYFL
          PAP.RG.PHVT..TPDYFL
Retrocopy PAPHRGKPHVTHCTPDYFL

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_2441 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 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002653	1 retrocopy	retro_acar_69,
Callithrix jacchus	ENSCJAG00000013634	2 retrocopies	retro_cjac_1346, retro_cjac_4113,
Homo sapiens	ENSG00000113575	1 retrocopy	retro_hsap_369,
Nomascus leucogenys	ENSNLEG00000026729	1 retrocopy	retro_nleu_2441 ,
Otolemur garnettii	ENSOGAG00000009695	2 retrocopies	retro_ogar_3414, retro_ogar_921,
Rattus norvegicus	ENSRNOG00000005389	5 retrocopies	retro_rnor_1263, retro_rnor_1264, retro_rnor_1265, retro_rnor_1266, retro_rnor_817,
Sarcophilus harrisii	ENSSHAG00000016632	3 retrocopies	retro_shar_313, retro_shar_428, retro_shar_471,
Ictidomys tridecemlineatus	ENSSTOG00000010560	1 retrocopy	retro_itri_258,