RetrogeneDB ID: retro_nleu_1107

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397281.1:17245937..17247118(-)
• Located in intron of: ENSNLEG00000009878

Retrocopy information

• Ensembl ID: ENSNLEG00000009882
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_nleu_1107
ATGTCTCACAGAAAGTTCTCCGCTGCCAGACATGGGTCCCTTGGCTTCCTGCCTCAGAAGCGCAGCAGCAGGCATCGTGG
GAAGGTGAAGAGCTTCCCAAGGATGATCCGTCCAAGCTGGTCCACCTCACGGCCTTCTTGGGATACAAGGCTGGCATGAC
TCACATCGTGCGGGAAGTCGACAGGCCAGGATCCAAGGTGAACAAGAAGGAGGTGGTGGAGGCTGTGACCATTGTGGAGA
CGCCACCCATGGTGGTTGTGGGCATTGTGGGCTACGTGGAAACCCCTCGAGGCCTCCGGACCTTCAAGACTGTCTTCGCT
GAGCACATCAGTGATGAATGCAAGAGGTGTTTCTATAAGAATTGGCATAAATCTAAGAAGAAGGCCTTTACCAAGTACTG
CAAGAAATGGCAGGATGAGGATGGCAAGAAGCAGCTGGAGAAGGACTTCAGCAGCATGAAGAAGTATTGCCAAGTCATCC
GTGTCATTGCCCACACCCAGATGCGCCTGCTTCCTCTGCGCCAGAAGGCGGCCCACCTGATGGAGATCCAGGTGAATGGA
GGCACCGTGGCCGAGAAGCTGGACTGGGCCCGCGAGAGGCTCGAGCAGCAGGTACCTGTGAACCAAGTGTTTGGGCAGGA
TGAGATGATCGACGTCATCGGGGTGACCAAGGGCAAAGGCTACAAAGGGGTCACCAGTCGTTGGCACACCAAGAAGCTGC
CCCGCAAGACCCACCGAGGCCTGCGCAAGGTGGCCTGTATTGGGGCACGGCATCCTGCTCGTGTAGCCTTCTCTGTGGCA
CGTGCTGGGCAGAAAGGCTACCATCACCGCACTGAGATCAACAAGAAGATCTGTAAGATTGGCCAGGGCTACCTTATCAA
GGACGGCAAGTTGATCGAGAACAATGCCTCCACTGACTATGACCTGTCTGACAAGAGCATCAACCCTCTGGGTGGCTTTG
TCCACTATGGTGAAGTGACCAATGACTTTGTCAAGCTGAAAGGCTGTGTGGTGGGAACCAAGAAACGGGTGCTCACCCTC
CGCAAGTCCTTGCTGGTGCAGACGAAGCGGTGGGCTCTGGAGAAGATTGACCTTAAGTTCATTGACACCACCTCCAAGTT
TGGCCATGGCCGCTTCCAGACCATGGAGGAGAAGAAAGCATTCATGGGACCAGTCAAGAAA

Alignment

ORF - retro_nleu_1107 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.22 %
• Parental protein coverage: 96.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSHRKFSAPRHGHLGFLPHKRSRRHRGKVKTWPR-DDPSQPVHLTAFLGYKAGMTHTLREVHRPGLKISK
          MSHRKFSA.RHG.LGFLP.KRS.RHRGKVK..PR.DDPS..VHLTAFLGYKAGMTH..REV.RPG.K..K
Retrocopy MSHRKFSAARHGSLGFLPQKRSSRHRGKVKSFPR<DDPSKLVHLTAFLGYKAGMTHIVREVDRPGSKVNK

Parental  REEVEAVTIVETPPVVVVGVVGYVATPRGLRSFKTIFAEHLSDECRRRFYKDWHKSKKKAFTKACKRWRD
          .E.VEAVTIVETPP.VVVG.VGYV.TPRGLR.FKT.FAEH.SDEC.R.FYK.WHKSKKKAFTK.CK.W.D
Retrocopy KEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRCFYKNWHKSKKKAFTKYCKKWQD

Parental  TDGKKQLQKDFAAMKKYCKVIRVIVHTQMKLLPFRQKKAHIMEIQLNGGTVAEKVAWAQARLEKQVPVHS
          .DGKKQL.KDF..MKKYC.VIRVI.HTQM.LLP.RQK.AH.MEIQ.NGGTVAEK..WA..RLE.QVPV..
Retrocopy EDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKAAHLMEIQVNGGTVAEKLDWARERLEQQVPVNQ

Parental  VFSQSEVIDVIAVTKGRGVKGVTSRWHTKKLPRKTHKGLRKVACIGAWHPARVGCSIARAGQKGYHHRTE
          VF.Q.E.IDVI.VTKG.G.KGVTSRWHTKKLPRKTH.GLRKVACIGA.HPARV..S.ARAGQKGYHHRTE
Retrocopy VFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKVACIGARHPARVAFSVARAGQKGYHHRTE

Parental  LNKKIYRIGRGPHMEDGKLVKNNASTSYDVTAKSITPLGGFPHYGEVNNDFVMLKGCIAGTKKRVITLRK
          .NKKI..IG.G....DGKL..NNAST.YD...KSI.PLGGF.HYGEV.NDFV.LKGC..GTKKRV.TLRK
Retrocopy INKKICKIGQGYLIKDGKLIENNASTDYDLSDKSINPLGGFVHYGEVTNDFVKLKGCVVGTKKRVLTLRK

Parental  SLLVHHSRQAVENIELKFIDTTSKFGHGRFQTAQEKRAFMGPQKK
          SLLV...R.A.E.I.LKFIDTTSKFGHGRFQT..EK.AFMGP.KK
Retrocopy SLLVQTKRWALEKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPVKK

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_1107 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,