RetrogeneDB ID: retro_nleu_1673

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397303.1:6637000..6638174(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL3L
• Ensembl ID: ENSNLEG00000008850
• Aliases: None
• Description: None

Sequence

>retro_nleu_1673
ATGTCTCACGGAAGGTTCTCTGCTCCCAGACATGGGTCCCTCGGCTGCCTGCCTCAGAAGCGCAGCGGGAAGCATCATGG
GAAGGTGAAGAGCTTTCCTAAGGATGACCCTTCCAAGCTGGTCCACCACACAGCCTTCCTGGGATACAAGGCTGGCATGA
CCAACATTGTGCGGGAAGTCGACAGGCCAGGATCCAAGGTGAAGAAGAAGGAAGTGGTAGAGGCTGTGACCATTGTGGAG
ACACCACCCGTGGTGGTTGTGGGCACTGTGGGCTACGTGGAAACCCCTCGAGGCCTCCAGACCTTCAAGACTGTCTTCAC
TGAGCACATCAGCAATGCGTGCAAGAGATATTTCTATAAAAACTGGCATAAATCTAAGAAGAAGGCCTTTACCAAGTACT
GCAAGAAATGTCAGGATGAGGATGGCAAGAAGCAGCTGGAGAAGGACTTCAGCAGCATGAAGAGGTACCGCCAAGTCATC
TGCATCATTGCCTACACCCAGATGTGCCTGCTTCCTCTGCGCCAGAGGAAGGCCCACCTGACAGAGATCCAGGTAAAGGG
AGGCACCGTGGCCAAGAAGCTGGACTGGGCCCACGAGAGGCTCGAGCAGCAGGTACCTGTGAAAAAAGTGTTTGGGCAGG
ACGAGATGATCGACGTCATCGGGTTGACCAAGGGCAACGGCTACAAAGGGGTCACCAGTCGTTGGCACACCAAGAAGCTG
CCCCGCAAGACCCACCGAGGCCTGTGCAAGGTAGCCTGTATTGGGGCACAGCATCCTGCCCCTGTGGCCTTCCCTGTGGC
ACGCGTTTGGCAGAAAGGCTACCATCACCGCACTGAGATCAACAAGAAGATCTATAAGATCAGACAGGGATACTTTATCA
AGGACAGCAAACTGATCAAGAACAATGCCTCCACTGACTATGACCTGTCTGACAAGCCACCCTCTGGGTGCCTTTGTCCA
CTATGAAGTGACCAATGACTTTGTCATGCTGAAAGACTGTGTGGTGGACACCAAGAAGCAAGTGCTCGCCCTTCACAAGT
CCTTGCCAGTGCCAACCAAACGGCGGGCTCTGGAGAAGACTGACCTTAAGTTCATTGACACCACCTCCAAGTTTGGCCAT
GGCTGCTTCCAAACCATGAAGGAGAGGACAGCATTCATGGCACCACTCAAGAAA

Alignment

ORF - retro_nleu_1673 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.34 %
• Parental protein coverage: 96.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSHRKFSAPRHGHLGFLPHKRSRRHRGKVKTWPRDDPSQPVHLTAFLGYKAGMTHTLREVHRPGLKISKR
          MSH..FSAPRHG.LG.LP.KRS..H.GKVK..P.DDPS..VH.TAFLGYKAGMT...REV.RPG.K..K.
Retrocopy MSHGRFSAPRHGSLGCLPQKRSGKHHGKVKSFPKDDPSKLVHHTAFLGYKAGMTNIVREVDRPGSKVKKK

Parental  EEVEAVTIVETPPVVVVGVVGYVATPRGLRSFKTIFAEHLSDECRRRFYKDWHKSKKKAFTKACKRWRDT
          E.VEAVTIVETPPVVVVG.VGYV.TPRGL..FKT.F.EH.S..C.R.FYK.WHKSKKKAFTK.CK...D.
Retrocopy EVVEAVTIVETPPVVVVGTVGYVETPRGLQTFKTVFTEHISNACKRYFYKNWHKSKKKAFTKYCKKCQDE

Parental  DGKKQLQKDFAAMKKYCKVIRVIVHTQMKLLPFRQKKAHIMEIQLNGGTVAEKVAWAQARLEKQVPVHSV
          DGKKQL.KDF..MK.Y..VI..I..TQM.LLP.RQ.KAH..EIQ..GGTVA.K..WA..RLE.QVPV..V
Retrocopy DGKKQLEKDFSSMKRYRQVICIIAYTQMCLLPLRQRKAHLTEIQVKGGTVAKKLDWAHERLEQQVPVKKV

Parental  FSQSEVIDVIAVTKGRGVKGVTSRWHTKKLPRKTHKGLRKVACIGAWHPARVGCSIARAGQKGYHHRTEL
          F.Q.E.IDVI..TKG.G.KGVTSRWHTKKLPRKTH.GL.KVACIGA.HPA.V....AR..QKGYHHRTE.
Retrocopy FGQDEMIDVIGLTKGNGYKGVTSRWHTKKLPRKTHRGLCKVACIGAQHPAPVAFPVARVWQKGYHHRTEI

Parental  NKKIYRIGRGPHMEDGKLVKNNASTSYDVTAKSITPLG-GFPHYGEVNNDFVMLKGCIAGTKKRVITLRK
          NKKIY.I..G....D.KL.KNNAST.YD...K...P.G..F.HY.EV.NDFVMLK.C...TKK.V..L.K
Retrocopy NKKIYKIRQGYFIKDSKLIKNNASTDYDLSDK--PPSG>AFVHY-EVTNDFVMLKDCVVDTKKQVLALHK

Parental  SLLVHHSRQAVENIELKFIDTTSKFGHGRFQTAQEKRAFMGPQKK
          SL.V...R.A.E...LKFIDTTSKFGHG.FQT..E..AFM.P.KK
Retrocopy SLPVPTKRRALEKTDLKFIDTTSKFGHGCFQTMKERTAFMAPLKK

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_1673 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 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008489	1 retrocopy	retro_amel_1881,
Nomascus leucogenys	ENSNLEG00000008850	9 retrocopies	retro_nleu_1107, retro_nleu_1130, retro_nleu_1249, retro_nleu_1305, retro_nleu_1673 , retro_nleu_1824, retro_nleu_2046, retro_nleu_2060, retro_nleu_3126,
Nomascus leucogenys	ENSNLEG00000015234	2 retrocopies	retro_nleu_1038, retro_nleu_1449,
Pongo abelii	ENSPPYG00000006973	1 retrocopy	retro_pabe_2854,
Pan troglodytes	ENSPTRG00000007617	12 retrocopies	retro_ptro_1439, retro_ptro_1473, retro_ptro_1753, retro_ptro_2150, retro_ptro_2339, retro_ptro_2462, retro_ptro_2501, retro_ptro_2646, retro_ptro_2741, retro_ptro_2767, retro_ptro_3163, retro_ptro_916,
Ictidomys tridecemlineatus	ENSSTOG00000012921	2 retrocopies	retro_itri_1344, retro_itri_867,