RetrogeneDB ID: retro_nleu_197

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397261.1:69727456..69728472(+)
• Located in intron of: ENSNLEG00000017941

Retrocopy information

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

Parental gene information

• Parental gene symbol: FXR1
• Ensembl ID: ENSNLEG00000005928
• Aliases: None
• Description: None

Sequence

>retro_nleu_197
ATGATGAAAGGAGAATTTTATGTCATTGAATATACTGCTTGTGACGCTACTTACAATGAAATAGTCACATTTGAACAACT
TTGGCCTGTCAATAAAAATAAAACCGTCAAAAAAAATACCTTCTTTAAATGCACAGTGGATTTTCCTGAGGATCTGAGAG
AGGCGTGTGCTAATGAAAATGCACATAAAGATTTTAAGAAAGCAGTAGGAGCATGCAGAATTTTTTACCATCCAGAATCA
ACACAGCTAATGATACTGTCTGCCAGTGAAGCAACTGTGAAGAAAGTAAACATCTTAAGTGACATGCATTTGTGAAGTAT
TTGTATGAAGCTGATGCTTATGACCAGAAATGAAGAGATCACTAAGCATTCAGAATGCACAAAACAACTTGCAGCGGCTT
TTCAGGAGGAATTTGTTGTGAGAGAAAATTTAATGGGTGTGGCAATAGGAACACATGGTAGTAACATTCAGCAAGCTAGG
AAGGTTCCTGGAGTCACCGCATTGAGCTAGATGAAGACACTGGAACATTTAGAATCTACAGAGAGAGTGTTGATGCTGTA
AAAAAGGCTAGAGGTTTCTTGGAATTTGTGGAGGATTTTATTCAGGTTTCTAAGAATCTCACGGGAAAAGTAATTGGAAA
AAATGGCAAAGTTATCCAAGAAACAGTGGACAAATCTGATATGGTTCGGGTGATAATTGAAGGTGACAGTGAAAATAAAC
TACCCAGAGAAGATGGTATGATTCCATTTGTGTTTGTTGGCACTAAAGAAACCACTGGAAATGTGCAAGTTCTTTTAGAG
TACCATATTGCTTATCTAAAGGAAGTAGAACAGCTAAGAATAGAATGCCTACAGATTGATGAGCAGCCATAACAGATTGG
TTCTAGGTCTTATAGTGGAAGAGGCAGAGGTTGTCAGGGCCCTAATTACACCTCCGGTTATGGTACAAATTCTGAGCTGT
CTAACCCCTCTGAAATAGAATCTGAGGATAAAGACAAGCTGAGTGATTGGTCATTG

Alignment

ORF - retro_nleu_197 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.47 %
• Parental protein coverage: 63.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MMKGEFYVIEYAACDATYNEIVTFERLRPVNQNKTVKKNTFFKCTVDVPEDLREACANENAHKDFKKAVG
          MMKGEFYVIEY.ACDATYNEIVTFE.L.PVN........TFFKCTVD.PEDLREACANENAHKDFKKAVG
Retrocopy MMKGEFYVIEYTACDATYNEIVTFEQLWPVNXXXXXXXXTFFKCTVDFPEDLREACANENAHKDFKKAVG

Parental  ACRIFYHPETTQLMILSASEATVKRVNILSDMHLRSIRTKLMLMSRNEEATKHLECTKQLAAAFHEEFVV
          ACRIFYHPE.TQLMILSASEATVK.VNILSDMHL.SI..KLMLM.RNEE.TKH.ECTKQLAAAF.EEFVV
Retrocopy ACRIFYHPESTQLMILSASEATVKKVNILSDMHL*SICMKLMLMTRNEEITKHSECTKQLAAAFQEEFVV

Parental  REDLMGLAIGTHGSNIQQARKVPGVTA-IELDEDTGTFRIYGESADAVKKARGFLEFVEDFIQVPRNLVG
          RE.LMG.AIGTHGSNIQQARKVPGVTA.IELDEDTGTFRIY.ES.DAVKKARGFLEFVEDFIQV..NL.G
Retrocopy RENLMGVAIGTHGSNIQQARKVPGVTA<IELDEDTGTFRIYRESVDAVKKARGFLEFVEDFIQVSKNLTG

Parental  KVIGKNGKVIQEIVDKSGVVRVRIEGDNENKLPREDGMVPFVFVGTKESIGNVQVLLEYHIAYLKEVEQL
          KVIGKNGKVIQE.VDKS..VRV.IEGD.ENKLPREDGM.PFVFVGTKE..GNVQVLLEYHIAYLKEVEQL
Retrocopy KVIGKNGKVIQETVDKSDMVRVIIEGDSENKLPREDGMIPFVFVGTKETTGNVQVLLEYHIAYLKEVEQL

Parental  RMERLQIDEQLRQIGSRSYSGRGRGRRGPNYTSGYGTNSELSNPSETESERKDELSDWSL
          R.E.LQIDEQ..QIGSRSYSGRGRG..GPNYTSGYGTNSELSNPSE.ESE.KD.LSDWSL
Retrocopy RIECLQIDEQP*QIGSRSYSGRGRGCQGPNYTSGYGTNSELSNPSEIESEDKDKLSDWSL

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_197 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000012105	1 retrocopy	retro_mmul_859,
Nomascus leucogenys	ENSNLEG00000005928	1 retrocopy	retro_nleu_197 ,
Ochotona princeps	ENSOPRG00000009223	2 retrocopies	retro_opri_61, retro_opri_779,
Pan troglodytes	ENSPTRG00000015656	1 retrocopy	retro_ptro_691,