RetrogeneDB ID: retro_nleu_1896

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397314.1:1225356..1225831(-)
• Located in intron of: ENSNLEG00000008297

Retrocopy information

• Ensembl ID: ENSNLEG00000008309
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CNIH
• Ensembl ID: ENSNLEG00000012704
• Aliases: None
• Description: None

Sequence

>retro_nleu_1896
TTCTCCGCTGGTACCGGCGCCTCTCCCCGCTCCTCCCCAGCCATGGCATTCACGTTCGTGGCCTTCTGCTACATGCTCTC
GCTGCTGCTCACTGCCGCACTCATCTTCTTCGCTATTTGGCACATTATTGCATTTGATGAACTGAAGACTGATTACAAGA
ATCCTACAGACCAGTGTTAATACCCTGAATCCACTTGTACTCCCAGAGTACCTCATCGACGCTTTCTTCTGTGTCATGTT
TCTTTGTGCAGCAGAGTGGCTTACACTGGGTCTCAATATGCCCCTTTTGACATATCATATTTGGAGGTATATGAGTAGAC
CAGTGACGAGTGGCCCAGGACTCTATGACCCTACAACCATCATGAATGCAGACATTCTAGCATATTGTCAGAAGGAAGGA
TGGTGCGAATTAGCTTTTTATCTTCTAGCATTTTTTTACTACCTATACGGCATGATCTATGTTTTGGTGAGCTCT

Alignment

ORF - retro_nleu_1896 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.38 %
• Parental protein coverage: 75. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FSAGTGASPRSSSPAMAFTFAAFCYMLALLLTAALIFFAIWHIIAFDELKTDYKNPIDQC-NTLNPLVLP
          FSAGTGASPRSS.PAMAFTF.AFCYML.LLLTAALIFFAIWHIIAFDELKTDYKNP.DQC.NTLNPLVLP
Retrocopy FSAGTGASPRSS-PAMAFTFVAFCYMLSLLLTAALIFFAIWHIIAFDELKTDYKNPTDQC>NTLNPLVLP

Parental  EYLIHAFFCVMFLCAAEWLTLGLNMPLLAYHIWRYMSRPVMSGPGLYDPTTIMNADILAYCQKEGWCKLA
          EYLI.AFFCVMFLCAAEWLTLGLNMPLL.YHIWRYMSRPV.SGPGLYDPTTIMNADILAYCQKEGWC.LA
Retrocopy EYLIDAFFCVMFLCAAEWLTLGLNMPLLTYHIWRYMSRPVTSGPGLYDPTTIMNADILAYCQKEGWCELA

Parental  FYLLAFFYYLYGMIYVLVSS
          FYLLAFFYYLYGMIYVLVSS
Retrocopy FYLLAFFYYLYGMIYVLVSS

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_1896 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031178	2 retrocopies	retro_cfam_658, retro_cfam_697,
Callithrix jacchus	ENSCJAG00000007306	1 retrocopy	retro_cjac_103,
Equus caballus	ENSECAG00000026814	1 retrocopy	retro_ecab_685,
Loxodonta africana	ENSLAFG00000014841	1 retrocopy	retro_lafr_963,
Nomascus leucogenys	ENSNLEG00000012704	1 retrocopy	retro_nleu_1896 ,
Nomascus leucogenys	ENSNLEG00000013549	1 retrocopy	retro_nleu_514,
Otolemur garnettii	ENSOGAG00000024582	1 retrocopy	retro_ogar_2271,
Ochotona princeps	ENSOPRG00000005287	4 retrocopies	retro_opri_198, retro_opri_269, retro_opri_366, retro_opri_894,
Tupaia belangeri	ENSTBEG00000010265	3 retrocopies	retro_tbel_2080, retro_tbel_3728, retro_tbel_572,
Tarsius syrichta	ENSTSYG00000011295	1 retrocopy	retro_tsyr_1540,
Tursiops truncatus	ENSTTRG00000008259	1 retrocopy	retro_ttru_261,