RetrogeneDB ID: retro_nleu_1034

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397279.1:23105841..23106392(+)
• Located in intron of: ENSNLEG00000017561

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAP1B
• Ensembl ID: ENSNLEG00000003573
• Aliases: None
• Description: None

Sequence

>retro_nleu_1034
ATGCATGAGTATAAGCTAATCATTCTTAGCCCAGGAGGCGTCGGAAAGTCTGCTTTGAATGTACAATTTGTTCAAGGAAT
TTTTGTTGAAAAATATGATCCTATGATAGAAGATTCTTATAGAAAGCAAGTTGAAGTAGATGCACAACAGTGTATGCTTG
CAATCTTGGATACTGCAGGAACGGAACAATTTATAGCGAGGAGGGATTTGTACATGAGAAATGGACAAGGCTTTGCATTA
GTTTATTCCATCACAGCACAGTCCACATTTAATGATTTGAAAGACTTGAGAGAACAGATTCTTCCAGTTAAAGACACTGA
TGATGTTCCAGTGATTATTGTTGGTAATAAGTAGGATTGGAAGATGAAAGAGTTGTAGGGAAGGAACAAGGTCAAAATCT
AGCAAGACAATGGAACAACTGTGCATTCTTAGATTCTTCTACAAAATCAAAAATAAATGTTAATGGGATCTTTTATAACC
TAGTGCGGCAGATTAACAGAAAAACTCCAGTGCCTGGGAAGGCTCGCAAAAAGTCATCATGTCAGCTGCTT

Alignment

ORF - retro_nleu_1034 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDL
          M.EYKL..L..GGVGKSAL.VQFVQGIFVEKYDP.IEDSYRKQVEVDAQQCML.ILDTAGTEQF.A.RDL
Retrocopy MHEYKLIILSPGGVGKSALNVQFVQGIFVEKYDPMIEDSYRKQVEVDAQQCMLAILDTAGTEQFIARRDL

Parental  YMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCD-LEDERVVGKEQGQNLARQWN
          YM.NGQGFALVYSITAQSTFNDL.DLREQIL.VKDTDDVP.I.VGNK.D.LEDERVVGKEQGQNLARQWN
Retrocopy YMRNGQGFALVYSITAQSTFNDLKDLREQILPVKDTDDVPVIIVGNK*D<LEDERVVGKEQGQNLARQWN

Parental  NCAFLESSAKSKINVNEIFYDLVRQINRKTPVPGKARKKSSCQLL
          NCAFL.SS.KSKINVN.IFY.LVRQINRKTPVPGKARKKSSCQLL
Retrocopy NCAFLDSSTKSKINVNGIFYNLVRQINRKTPVPGKARKKSSCQLL

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_1034 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 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Callithrix jacchus	ENSCJAG00000007261	3 retrocopies	retro_cjac_1435, retro_cjac_2371, retro_cjac_607,
Cavia porcellus	ENSCPOG00000008272	4 retrocopies	retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Gorilla gorilla	ENSGGOG00000025649	1 retrocopy	retro_ggor_2836,
Loxodonta africana	ENSLAFG00000016460	1 retrocopy	retro_lafr_482,
Mus musculus	ENSMUSG00000052681	1 retrocopy	retro_mmus_1370,
Nomascus leucogenys	ENSNLEG00000003055	1 retrocopy	retro_nleu_935,
Nomascus leucogenys	ENSNLEG00000003573	2 retrocopies	retro_nleu_1034 , retro_nleu_481,
Nomascus leucogenys	ENSNLEG00000004018	1 retrocopy	retro_nleu_1069,
Nomascus leucogenys	ENSNLEG00000005266	1 retrocopy	retro_nleu_338,
Otolemur garnettii	ENSOGAG00000005746	2 retrocopies	retro_ogar_2260, retro_ogar_272,
Sarcophilus harrisii	ENSSHAG00000011497	1 retrocopy	retro_shar_425,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,
Tupaia belangeri	ENSTBEG00000013380	4 retrocopies	retro_tbel_2145, retro_tbel_4650, retro_tbel_4658, retro_tbel_613,