RetrogeneDB ID: retro_nleu_2561

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397372.1:4936100..4937216(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC19A3
• Ensembl ID: ENSNLEG00000013501
• Aliases: None
• Description: None

Sequence

>retro_nleu_2561
TCACTGGCTCCCAGGTGGCCTACTGTATCAACCCATGCAGCATGGTCAGCCCTGAGACACTGTCAGGAAGTGAGAGGCCA
CCATAGGAGTGTCATGCTAACAGCCAACCCAGCGGCCCCCATGAAGGCTGACGCTTGGCATCCCTGGAGAGTGGGTCACA
CTTTTACCTCATCGCATAGCCATAGTCTCTGCCTCCACAGCCTTCATTTTCTCACTTTTTCTATCAATGCCCAAGAAAAG
CATGTTTTTCCATGCAAAACCCAGCAAAGAAATAAGGAAGTCCCCAAGCCTGTGTGCAGAGTTAAAGGAACCTCGTGAGA
GTAAAGCACTAGGCTGTGAAGGGGAGAAATCCACTTGGGAAAAGCCCACCACTTCGGGGAACCTGGATGACGGTCCGCAG
AACATAGTGCCACAAACAGTGACTCTGAAAGTTCGTGTTCCATGGTTTCAAGATTTGAAGTAGTGTTACTCCTCAGAGGC
CTTTGTTACTAAATCCCCAGGGCAGGCTTTTTCCACCACAGGTTTTAACCTAGCTTTGAACTATGTTCAAGTCCTATGAG
GTTGCAAAGCACCACCCCAATATTCTTATACCTATAATGGGGCACAGAAGCTACTGAAGCATTTGGTAGGGCTGTGGCTG
CCTGTGCAGAGGGCTATGTGAAAATCAACTGGAGTCTCCTGGAGAGTGGGCTCTGGAAGTCTCCTCAGTCATCAACGCAG
GCTCTTGACCTCTCACGCGCTACATGACCAACGTCTACGCAGGCTATGTGGGCTATGTGCGATTCAAGTCCAACTATGTG
CTGCTTCTAACCCAGGCAGTATTCCAGACTGCAGTCAAGCTGAGCGTGGAATGTGTATCCTGGTGTCCGGATTCCACACC
TCACTGCCTTGGTGATTCAGCAGACCCTCATCACTGTGGCCGCAATTCATCAGAGAGGGCTCAGCCTGTGATCAGCATTC
AGTTTGTAGTTTACAGGAGTTATTTTGCAGTCATTTCTAGAATTTTCCTAATAAGAATATCTAATGCCTATCAACAAATG
CCAAGAAGAAGGAGTTCAGAGCCCTGCTATGAGTCAGAACCCAGACGGGCCGCACCCAAAGGAGCTGAGCAGTATC

Alignment

ORF - retro_nleu_2561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.33 %
• Parental protein coverage: 76.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  SRPPRW-AYYAYIYSVVSP-KHYR-VSGYCRSVTLAAYTAASVLAQL-LVSLVNLSYFYL-HVISLASVS
          S..PRW.AY.....S.VSP..H...V.G..RSV.L.A..AA...A...L.SL...S.FYL.H.I...S.S
Retrocopy SLAPRW<AYCINPCSMVSP>RHCQEVRGHHRSVMLTANPAAPMKADA<LASLESGSHFYL<HRIAIVSAS

Parental  VAFLFSLFLPMPKKSMFFHAKPSREIKKSPSVNPVLEETHEGEAPGCKEQKPTSEILSTSGKQSKGQLNS
          .AF.FSLFL.MPKKSMFFHAKPS.EI.KSPS....L.E..E..A.GC...K.T.E...TSG....G..N.
Retrocopy TAFIFSLFLSMPKKSMFFHAKPSKEIRKSPSLCAELKEPRESKALGCEGEKSTWEKPTTSGNLDDGPQN-

Parental  LKPSNVTVDVFVQWFQDLKECYSSKRLFYWSLWWAFATAGFNQVLNYVQILWDYKAPSQDSSIYNGA-VE
          ..P..VT..V.V.WFQDLK.CYSS......S...AF.T.GFN..LNYVQ.L...KAP.Q.S..YNGA..E
Retrocopy IVPQTVTLKVRVPWFQDLK*CYSSEAFVTKSPGQAFSTTGFNLALNYVQVL*GCKAPPQYSYTYNGA<TE

Parental  AIATFGGAVAAFAVGYVKVNWDLL-GELALAVFSVVNAGSLFLMHYTANIWACYAGYLIFKSSYMLLITI
          A...FG.AVAA.A.GYVK.NW.LL.GE.AL.V.SV.NAGS..L..Y..N..A.Y.GY..FKS.Y.LL.T.
Retrocopy ATEAFGRAVAACAEGYVKINWSLL<GEWALEVSSVINAGS*PLTRYMTNVYAGYVGYVRFKSNYVLLLTQ

Parental  AVFQIAVNLNVERYA-LVFGINTFI-ALVI-QTIMTVIVVDQRGLNL-PVSIQFLVYGSYFAVIAGIFLM
          AVFQ.AV.L.VE....LV.G..T...ALVI.QT..TV....QRGL.L...SIQF.VY.SYFAVI..IFL.
Retrocopy AVFQTAVKLSVECVS<LVSGFHTSL<ALVIQQTLITVAAIHQRGLSL<VISIQFVVYRSYFAVISRIFLI

Parental  RSMYIIYSAKSQKDIQSPAPSENP-DVSHPEEESNI
          R.....Y..........P.....P.D..HP.E.S.I
Retrocopy R-ISNAYQQMPRRRSSEPCYESEP>DGPHPKELSSI

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_2561 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000135917	1 retrocopy	retro_hsap_3732,
Gorilla gorilla	ENSGGOG00000004344	1 retrocopy	retro_ggor_2518,
Monodelphis domestica	ENSMODG00000021220	1 retrocopy	retro_mdom_955,
Mustela putorius furo	ENSMPUG00000001374	1 retrocopy	retro_mputfur_1211,
Nomascus leucogenys	ENSNLEG00000013501	1 retrocopy	retro_nleu_2561 ,
Pongo abelii	ENSPPYG00000013242	1 retrocopy	retro_pabe_3209,
Pan troglodytes	ENSPTRG00000028998	1 retrocopy	retro_ptro_2526,