RetrogeneDB ID: retro_nleu_908

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397276.1:11805621..11806808(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RTN4IP1
• Ensembl ID: ENSNLEG00000013349
• Aliases: None
• Description: None

Sequence

>retro_nleu_908
ATGGAATTTCTGAAGACTTGTGTACTTAGAAGAAACGCAGATACGTGGTTTGCTTCTGGAGAAGCAAAGTTGTCCAAAAG
CCTTCCATTAAAAGGATTTGTACTACCTCTCCAAGGAGCACTGTCACGCCTGCTTGGGTGATAGATAAGTATGGGAAGAA
TGAAGTACTTCAATTCACTCAGAACATGATGATACCTATCATACACTATCCAAATGAAGTCATTGTGAAAGTTCACGCTG
CCAGTGTAAATCCTATAGACGTCAATATGGAAGTGGTTATGGAGCTACAGCTTTAAATATGAAGCTTAATCCTTTATACA
TGAAAATCAAAGGAGAAGAATTTCCTCTGACTCTTGTTTGGGATGTCTCTGGCATGGTGATGGAATGTGGGCTTGATGTG
AAGTACTTCAAGCCTGGAGAGGAGGTCTGGGCTGCAGTTCCTCCTTGGAAACAAGGCACTCTTTCAGAGTTTGTTGTAGT
CAGTGGAAATGAGGTCTCTCACAAACCCAAATCACTCACTCATATACCAAGCTGCCTCTTTGCCATATGTGGCTTTCACA
GCCTGGTCTGCCATAAACAAAGTTGGTGGCTTGAATGACAAGAATTGCACAGGAAAACGTGTTCTAATCTTAGGTGCTTC
AGGCGGAGTTGGTACTTTTGCTATACAGGTGATGAAAGCATGGGATGCTCATGTGACAGCAGTTTGTGCTCAAGATGCCA
GTGAATTTATAAAGAAGCTTGGGGCAGATGATGTAATTGGTTACAAATCTGGAAGTGTGGAAGAGCAGTTGAAATCCTTA
AAACTGTTTGATTTCATCCTTGATAATGTTGGCAGATCCACTGAAACATGGGCTCCAAATTTTCTCAATAAATGGTCAGG
AGCCACCTGTGTGACTTTGGTGAGTCCTTTCCTCCTGAACACGGACCGATTGGGCATAGCAGATGGCATGTTGCAGGCAG
GAGTCACTGTAGGTTTGAAGTCATTAAAGCATTTCTGGAAAGGAGTCCATTATCGCTGAGTGTTTTTCATGGCCAGTGGT
CCATGTTTAGGTGACATTGCAGAACTGGTGGATGAGGGAAAAATTTGGCCAGTTATTGAACAAACCTTTCCTTTTTCTAA
AGTTCCAGAAGCCTTCCTGAAGGTGGAAAGAGGACCCACATGAGGAAAGACTGTAATTAATGTTGTT

Alignment

ORF - retro_nleu_908 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MEFLKTCVLRRNACI-AACFWRSKVVQKPSVRRISTTSPRSTVMPAWVIDKYGKNEVLRFTQNMMMPIIH
          MEFLKTCVLRRNA.....CFWRSKVVQKPS..RI.TTSPRSTV.PAWVIDKYGKNEVL.FTQNMM.PIIH
Retrocopy MEFLKTCVLRRNADT<VVCFWRSKVVQKPSIKRICTTSPRSTVTPAWVIDKYGKNEVLQFTQNMMIPIIH

Parental  YPNEVIVKVHAASVNPIDVNMR-SGYGATALNMKRDPLHVKIKGEEFPLTLGRDVSGVVMECGLDVKYFK
          YPNEVIVKVHAASVNPIDVNM..SGYGATALNMK..PL..KIKGEEFPLTL..DVSG.VMECGLDVKYFK
Retrocopy YPNEVIVKVHAASVNPIDVNME<SGYGATALNMKLNPLYMKIKGEEFPLTLVWDVSGMVMECGLDVKYFK

Parental  PGDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHT-QAASLPYVALTAWSAINKVGGLNDKNCTGKR
          PG.EVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTH..QAASLPYVA.TAWSAINKVGGLNDKNCTGKR
Retrocopy PGEEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHI>QAASLPYVAFTAWSAINKVGGLNDKNCTGKR

Parental  VLILGASGGVGTFAIQVMKAWDAHVTAVCSQDASELVRKLGADDVIDYKSGSVEEQLKSLKPFDFILDNV
          VLILGASGGVGTFAIQVMKAWDAHVTAVC.QDASE...KLGADDVI.YKSGSVEEQLKSLK.FDFILDNV
Retrocopy VLILGASGGVGTFAIQVMKAWDAHVTAVCAQDASEFIKKLGADDVIGYKSGSVEEQLKSLKLFDFILDNV

Parental  GGSTETWAPDFLKKWSGATYVTLVTPFLLNMDRLGIADGMLQTGVTVGSKTLKHFWKGVHYRWAFFMASG
          G.STETWAP.FL.KWSGAT.VTLV.PFLLN.DRLGIADGMLQ.GVTVG.K.LKHFWKGVHYR..FFMASG
Retrocopy GRSTETWAPNFLNKWSGATCVTLVSPFLLNTDRLGIADGMLQAGVTVGLKSLKHFWKGVHYR*VFFMASG

Parental  PCLDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVERGHARGKTVINVV
          PCL.DIAELVD.GKI.PVIEQTFPFSKVPEAFLKVERG...GKTVINVV
Retrocopy PCLGDIAELVDEGKIWPVIEQTFPFSKVPEAFLKVERGPT*GKTVINVV

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_908 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000130347	1 retrocopy	retro_hsap_1030,
Gorilla gorilla	ENSGGOG00000008254	1 retrocopy	retro_ggor_814,
Nomascus leucogenys	ENSNLEG00000013349	1 retrocopy	retro_nleu_908 ,
Otolemur garnettii	ENSOGAG00000012703	1 retrocopy	retro_ogar_590,
Pongo abelii	ENSPPYG00000016882	1 retrocopy	retro_pabe_863,
Pan troglodytes	ENSPTRG00000018461	1 retrocopy	retro_ptro_705,