RetrogeneDB ID: retro_nleu_1628

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397301.1:16434602..16435815(-)
• Located in intron of: ENSNLEG00000005126

Retrocopy information

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

Parental gene information

• Parental gene symbol: MLF1IP
• Ensembl ID: ENSNLEG00000010967
• Aliases: None
• Description: None

Sequence

>retro_nleu_1628
CAGCCTCCCGGGCATGCAGGTCCATGATATTCAAAGAACATTTTGTGAAGAACACATTCTGTGAAATATAAAGCTGGTCA
AAAGTGCAAGCCTACCAATGTGTTTGATTTTCCTAATAATTCTGCCATCTCAAGAATTGGCAGGCTTGGTGAAAATGAGA
AAGATGAAGAACCTTATGAAACCGTTGATCCTCCTTTACACAGCTCATCTATGTATGCCAATGAAGAATTCTCCAAATAT
TGTGGATTATCTATCACTTCAACTCCTCCAGGAAAAGAAGCAAAAAGAAGCTCGAGCACTTCTGAAAATGAAGGAAGTGA
AAACAAATCTGCAAAAATGAGTGCAAAAAGCCAGGAGGAAAACTCAAACTCATGAGCGATGAGTCTGAAAGCACTGAAGA
AAGTGATGTGAAAAGAAAAGTTAAGTCAGTGGAGAAAATAAGGACCCAACAACACGAGGCTATTCCAACTACAGCATCTT
CAGCCCTTTCAGAGAAACCAGCTGACTCAGTCACTTCCAAAAAGATAGGACCCATTAGTGCGCAGCCATCTGTTGAAAAA
GACACACTGACAACAGAAAGTCAAGCAAAACCCAGAAAAAAGGGAATACATCTTATGGCAAAAGGAAGAAATCAAGAAGT
GAAGCCACAGACTCAGATATTTCCAATACTGTGCACATTTGGTGTCTGGAAGGAGAGAAAACTAACGACATCACGGAATT
GAATATTGTTTTGCCTGCATTTGCGAAAACCCTCGTCCAGTATAAACATAGAATAGAATCTAAAATTTGTAAGAAAGACA
TCAATAAATTTTATTTTAATAGTAAAGAAGAACTCAACAAAATGCTTAAAAAGTCCAGATATTGATAAATCTGAAAAAGA
AGAATGCTAAGGTAATTTCAGATATCAAAAAGAAATGACAGTGTTTGACTGAAGTCCAGGATGAACTGCTTTGGTTAGAG
CCACCAACTGAAACGACAACAAAATATTATGAACTTAAGGAGAGAACAGTCTTCCCTTAGGAATGCAGCTATTTCTTATC
TAATTCAAAACAACTCCGTCGGAAGTATTCAGATGTTCAGGAGAAAGAACCAAACGTAAAGGAAACATATGATTCATCCA
GCCTTCCAGGTGTTATTTAAAGCAGGAACACTTTTGGGAGCTGAAAACCATCTGTAAAATATCAACCATCAGTGAGAGAA
GCTCCTCCACCAG

Alignment

ORF - retro_nleu_1628 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.39 %
• Parental protein coverage: 98.08 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RPHRSEGTRRSKNTLERTHSMKDKAGQKCKPIDVFDFPDNSDVSSIGRLGENEKDEEPYETFDPPLHSTA
          .P....G...SKN.L.RTHS.K.KAGQKCKP..VFDFP.NS..S.IGRLGENEKDEEPYET.DPPLHS..
Retrocopy QPPGHAGP*YSKNIL*RTHSVKYKAGQKCKPTNVFDFPNNSAISRIGRLGENEKDEEPYETVDPPLHSSS

Parental  IYADEEEFSKHCGLSIPSTPPGKEAKRSSDTSGNEASEIESIKISAK-KPGRKLRPISDDSESTEESDTR
          .YA.EE.FSK.CGLSI.STPPGKEAKRSS.TS.NE.SE..S.K.SAK.KPG.KL...SD.SESTEESD..
Retrocopy MYANEE-FSKYCGLSITSTPPGKEAKRSSSTSENEGSENKSAKMSAK<KPGGKLKLMSDESESTEESDVK

Parental  RKVKSAEKISTQRHEVIRTTASSELSEKPAELVTSKKTGPLTAQPSVEKENLAIESQ-SKIQKKGKMSHD
          RKVKS.EKI.TQ.HE.I.TTASS.LSEKPA..VTSKK.GP..AQPSVEK..L..ESQ.SK.QKKG..S..
Retrocopy RKVKSVEKIRTQQHEAIPTTASSALSEKPADSVTSKKIGPISAQPSVEKDTLTTESQ<SKTQKKGNTSYG

Parental  KRKKSRSKAVGSDTSDIVHIWCPEGMKTSDIKELNIVLPEFEKTHLEHKQRVESKVCKAAIDTFCSNVKE
          KRKKSRS.A..SD.S..VHIWC.EG.KT.DI.ELNIVLP.F.KT....K.R.ESK.CK..I..F..N.KE
Retrocopy KRKKSRSEATDSDISNTVHIWCLEGEKTNDITELNIVLPAFAKTLVQYKHRIESKICKKDINKFYFNSKE

Parental  QLIKMLEES-QMLKNLKRKNAKMISDIEKKRQRMIEVQDELLRLEPQLKQLQTKYDELKER-KSSLRNVA
          .L.KML..S.Q.L.NLK.KNAK.ISDI.KK.Q...EVQDELL.LEP......TKY.ELKER..SSLRN.A
Retrocopy ELNKMLKKS<QILINLKKKNAKVISDIKKK*QCLTEVQDELLWLEPP-TETTTKYYELKER>QSSLRNAA

Parental  -YFLSNLKQLYQDYSDVQAKEPNIKETYDSSSLPALLFKARTLLGA-ESHLRNINHQLEKLLDQ
          .YFLSN.KQL...YSDVQ.KEPN.KETYDSSSLP......R...G..E.HL.NINHQ.EKLL.Q
Retrocopy <YFLSNSKQLRRKYSDVQEKEPNVKETYDSSSLPGVI-*SRNTFGS>ENHL*NINHQ*EKLLHQ

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_1628 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000151725	1 retrocopy	retro_hsap_1096,
Gorilla gorilla	ENSGGOG00000011892	1 retrocopy	retro_ggor_862,
Microcebus murinus	ENSMICG00000013084	1 retrocopy	retro_mmur_836,
Macaca mulatta	ENSMMUG00000012176	1 retrocopy	retro_mmul_850,
Nomascus leucogenys	ENSNLEG00000010967	1 retrocopy	retro_nleu_1628 ,
Oryctolagus cuniculus	ENSOCUG00000003903	1 retrocopy	retro_ocun_1174,
Pongo abelii	ENSPPYG00000015238	1 retrocopy	retro_pabe_979,
Pan troglodytes	ENSPTRG00000016643	1 retrocopy	retro_ptro_697,