RetrogeneDB ID: retro_nleu_1186

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397284.1:18903383..18904031(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000004301
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TSPAN6
• Ensembl ID: ENSNLEG00000007505
• Aliases: None
• Description: None

Sequence

>retro_nleu_1186
ATCACTGGCGTTATCCTTCTTGCAGTAGGCATTTGGGGCAAGGTGAGCCTGGAGAATTACTTTTCACTTTTAAATGAGAA
GGCCACCAATGTCCCCTTCGTGCTCATTGCTACTGGTACCGTCATTATTCTTTTGGGCACCTTTGGTTGTTTTGCTACCT
GCCGAGCTTCTGCATGGATGCTAAAACTGTATGCAATGTTTCTGACTCTCATTTTTTTGGTCGAACTGGTCGCTGCCATC
GTAGGATTTGTTTTCAGACATGAGATTAAGAATAGGTTTAAGAATAATTATGAGAAGGCTTTGAAGCAGTATAACTCTAC
AGGAGATTATAGAAGCCATGCAGTAGACAAGATCCAAAATACGTTGCATTGTTGTGGTGTCACCGATTATAGAGATTGGA
CAGATACTAATTATTACTCAGAAAAAGGATTTCCTAAGAGTTGCTGTAAACTTGAAGATTGTACTCCACAGAGAGATGCA
GACAAAGTAAACAATGAAGGTTGTTTTATAAAGGTGATGACCATTATAGAGTCAGAAATGGGAGTCGTTGCAGGACTTTC
CTTTGGAGTTGCTTGCTTCCAACTGATTGGAATCTTTCTCGCCTACTGCCTCTCTCGTGCCATAACAAATAACCAGTATG
AGATAGTG

Alignment

ORF - retro_nleu_1186 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.15 %
• Parental protein coverage: 88.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ITGVILLAVGIWGKVSLENYFSLLNEKATNVPFVLIATGTVIILLGTFGCFATCRASAWMLKLYAMFLTL
          ITGVILLAVGIWGKVSLENYFSLLNEKATNVPFVLIATGTVIILLGTFGCFATCRASAWMLKLYAMFLTL
Retrocopy ITGVILLAVGIWGKVSLENYFSLLNEKATNVPFVLIATGTVIILLGTFGCFATCRASAWMLKLYAMFLTL

Parental  IFLVELVAAIVGFVFRHEIKNSFKNNYEKALKQYNSTGDYRSHAVDKIQNTLHCCGVTDYRDWTDTNYYS
          IFLVELVAAIVGFVFRHEIKN.FKNNYEKALKQYNSTGDYRSHAVDKIQNTLHCCGVTDYRDWTDTNYYS
Retrocopy IFLVELVAAIVGFVFRHEIKNRFKNNYEKALKQYNSTGDYRSHAVDKIQNTLHCCGVTDYRDWTDTNYYS

Parental  EKGFPKSCCKLEDCTPQRDADKVNSEGCFIKVMTVIESEMGVVAGISFGVACFQLIGIFLAYCLSRAITN
          EKGFPKSCCKLEDCTPQRDADKVN.EGCFIKVMT.IESEMGVVAG.SFGVACFQLIGIFLAYCLSRAITN
Retrocopy EKGFPKSCCKLEDCTPQRDADKVNNEGCFIKVMTIIESEMGVVAGLSFGVACFQLIGIFLAYCLSRAITN

Parental  NQYEIV
          NQYEIV
Retrocopy NQYEIV

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_1186 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017521	3 retrocopies	retro_cfam_1600, retro_cfam_1609, retro_cfam_878,
Callithrix jacchus	ENSCJAG00000004288	1 retrocopy	retro_cjac_2306,
Echinops telfairi	ENSETEG00000012276	1 retrocopy	retro_etel_1987,
Loxodonta africana	ENSLAFG00000027296	1 retrocopy	retro_lafr_994,
Microcebus murinus	ENSMICG00000011370	1 retrocopy	retro_mmur_447,
Nomascus leucogenys	ENSNLEG00000003649	1 retrocopy	retro_nleu_1643,
Nomascus leucogenys	ENSNLEG00000007505	1 retrocopy	retro_nleu_1186 ,
Otolemur garnettii	ENSOGAG00000004869	1 retrocopy	retro_ogar_2827,
Sarcophilus harrisii	ENSSHAG00000000274	1 retrocopy	retro_shar_515,
Sus scrofa	ENSSSCG00000012481	1 retrocopy	retro_sscr_84,