RetrogeneDB ID: retro_nleu_1800

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397309.1:7485103..7485883(-)
• Located in intron of: ENSNLEG00000001931

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM22
• Ensembl ID: ENSNLEG00000010397
• Aliases: None
• Description: None

Sequence

>retro_nleu_1800
GACATGCCAAAGTCATGAAGACGTCAGAGAAGAGAAGAGTACTACATGCAGAATGTGGAGAGAGGGATTTCTAACTCTAA
TGGAAGACAGCCAGTTGGCCTGCTGGGGAAAGCCACATCCACTAGTGACATGCTAGACAAACTGGCCTGGACCATACCCT
ATTACTTAAAGAATAAGCCCCACATTTGCTCCTTCTGGGTGGAGGGATAGGGTAAGAGAGAAGAGGAGTTTTGATAGAGA
CATGAGAAGCCTACAGGTCCACATGATTCCCTTGCTGATCAGATATTAAAGACTGATATTATACAGTCAATGACCCTGTA
GCAGATAAGCTTCTATAGTAGGCTTCAGCCACGCCTCATCTGGAACTCCCAGAGGACAAGACTATCCCCACACTAGATGC
TGGTGATCCGGGTGATACCATTACTGAGACAGATCTTAAGAAATAATCTCTACCTATTTAGAGAGATCTGGACAATCCCT
GTTGTGCAGAGACAACGGTGTGCTTTTATCCAGGCTTCCACAGGGCAGGCTGCACAAGTGGCTGCAGAGAAGTCCTTTAA
TAAGTTAATCGTCAATGGCTGCAGACTAAGTGTAAAATGGGGAAGATCCCAGGCAGCCAGAGGAAAGGAAAATGACAGAA
CCCCAGACCTGGGGATCCAGCTAGAGCTGATTCCAGTACTGCCGGGAGCTCCTCCTCCTTCTGCAGCAGCAGATGCATCT
GCCAATGACTTCAACCTACCTCCAAGTGCTCCTACAGCTGTGGTGAACATTGCCTGGCCA

Alignment

ORF - retro_nleu_1800 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.55 %
• Parental protein coverage: 62.14 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DMPKS---DVNKEYYTQNMEREISNSDGTRPVGMLGKATSTSDMLLKLARTTPYYKRNRPHICSFWVKGE
          DMPKS.......EYY.QN.ER.ISNS.G..PVG.LGKATSTSDML.KLA.T.PYY..N.PHICSFWV.G.
Retrocopy DMPKS*RRQRREEYYMQNVERGISNSNGRQPVGLLGKATSTSDMLDKLAWTIPYYLKNKPHICSFWVEG*

Parental  CKRGEECPYRHEKPTDPDDPLADQ-NIKDRYYGINDPVADKLLKRASTMPRLDPPEDKTITTLYVGGLGD
          .KR.EE...RHEKPT.P.D.LADQ..IKD.YY..NDPVADKLL..AS..P.L..PEDKTI.TL..G..GD
Retrocopy GKREEEF**RHEKPTGPHDSLADQ<DIKD*YYTVNDPVADKLL**ASATPHLELPEDKTIPTLDAGDPGD

Parental  TITETD-LRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGRSQAARG
          TITETD.LRN..Y.F.EI.TI.VVQRQ.CAFIQ..T.QAA.VAAEKSFNKLIVNG.RL.VKWGRSQAARG
Retrocopy TITETD>LRNNLYLFREIWTIPVVQRQRCAFIQASTGQAAQVAAEKSFNKLIVNGCRLSVKWGRSQAARG

Parental  KEKEKDGTTDSGIKLEPVPGLPGALPPPPAAEEEASANYFNLPPSGPPAVVNIALP
          ..KE.D.T.D.GI.LE..P.LPGA..PPP.A...ASAN.FNLPPS.P.AVVNIA.P
Retrocopy --KENDRTPDLGIQLELIPVLPGA--PPPSAAADASANDFNLPPSAPTAVVNIAWP

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_1800 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000009040	2 retrocopies	retro_mluc_1453, retro_mluc_153,
Monodelphis domestica	ENSMODG00000009574	1 retrocopy	retro_mdom_186,
Nomascus leucogenys	ENSNLEG00000010397	2 retrocopies	retro_nleu_1691, retro_nleu_1800 ,
Ictidomys tridecemlineatus	ENSSTOG00000027197	1 retrocopy	retro_itri_1188,