RetrogeneDB ID: retro_nleu_1973

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397320.1:13915671..13916389(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000004596
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GRSF1
• Ensembl ID: ENSNLEG00000007721
• Aliases: None
• Description: None

Sequence

>retro_nleu_1973
ATGAAGAGCTTGTCTGTGGTAAATGATGGTGTGGTTCGTTTGAGAGGACTTCCTTATAGTTGCAATGAGAAAGACATTGT
AGACTTCTTTGCAGGACTGAGTATAGTTGACATTACTTTTGTGATGGACTACAGAGGGAGACGAAAAACGGGAAGCCTAT
GTGCAATTTGAAGAACCAGAAATGGCCAACCAAGCCCTGTTGAAACACAGGGAAGAAATTGGTAATCGATACATTGAGAT
ATTTCCAAGCAGAAGGAATGAAGTTCGAACACATGTTGGTTCTTATAAGGGAAAGAAAATCACATCTTTTCCTACTGCTA
AGTATATAACTGAGCCAGAAATGGTCTTTGAAGAACATGAAGTAAATGAGGATATTCAACCCATGACAGCTTTTGAAAGT
GAGAAGGAAATAGAATTGCCTGAGGAGGTGCCAGAAAAGCTTCCAGAGGCTGCTGGTTTTGGAACTACGTCTTCTCTGCA
TTTTGTCCACATGAGAGGATTACCTTTCCAAGCCAATGCCCAAGACATTATAAACTTTTTTGCTCCACTCAAGCCTGTTA
GAATCACCATGGAATACAGCTCCAGTAGGAAGGCCACTGGAGAAGCTGATGTGCACTTTGAGACCCATGAGGATGCTGTT
GCAGCGATGCTCAAGGATCGGTCCCACGTTCATCATAGGTATATTGAACTGTTCTTGAATTCATGTCCAAAAGGAAAA

Alignment

ORF - retro_nleu_1973 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.45 %
• Parental protein coverage: 75.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VKSSPVVNDGVVRLRGLPYSCNEKDIVDFFAGLNIVDITFVMDYRGRR-KTG-EAYVQFEEPEMANQALL
          .KS..VVNDGVVRLRGLPYSCNEKDIVDFFAGL.IVDITFVMDYRGRR.K.G.EAYVQFEEPEMANQALL
Retrocopy MKSLSVVNDGVVRLRGLPYSCNEKDIVDFFAGLSIVDITFVMDYRGRR<KNG<EAYVQFEEPEMANQALL

Parental  KHREEIGNRYIEIFPSRRNEVRTHVGSYKGKKITSFPTAKYITEPEMVFEEHEVNEDIQPMTAFESEKEI
          KHREEIGNRYIEIFPSRRNEVRTHVGSYKGKKITSFPTAKYITEPEMVFEEHEVNEDIQPMTAFESEKEI
Retrocopy KHREEIGNRYIEIFPSRRNEVRTHVGSYKGKKITSFPTAKYITEPEMVFEEHEVNEDIQPMTAFESEKEI

Parental  ELPKEVPEKLPEAADFGTTSSLHFVHVRGLPFQANAQDIINFFAPLKPVRITMEYSSSGKATGEADVHFE
          ELP.EVPEKLPEAA.FGTTSSLHFVH.RGLPFQANAQDIINFFAPLKPVRITMEYSSS.KATGEADVHFE
Retrocopy ELPEEVPEKLPEAAGFGTTSSLHFVHMRGLPFQANAQDIINFFAPLKPVRITMEYSSSRKATGEADVHFE

Parental  THEDAVAAMLKDRSHVHHRYIELFLNSCPKGK
          THEDAVAAMLKDRSHVHHRYIELFLNSCPKGK
Retrocopy THEDAVAAMLKDRSHVHHRYIELFLNSCPKGK

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_1973 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 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000007721	1 retrocopy	retro_nleu_1973 ,
Nomascus leucogenys	ENSNLEG00000026658	3 retrocopies	retro_nleu_1668, retro_nleu_28, retro_nleu_48,
Ictidomys tridecemlineatus	ENSSTOG00000011569	2 retrocopies	retro_itri_1828, retro_itri_523,
Tupaia belangeri	ENSTBEG00000010173	2 retrocopies	retro_tbel_3827, retro_tbel_987,
Tarsius syrichta	ENSTSYG00000008487	1 retrocopy	retro_tsyr_770,