RetrogeneDB ID: retro_nleu_350

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397263.1:18000996..18002146(-)
• Located in intron of: ENSNLEG00000005817

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF38B
• Ensembl ID: ENSNLEG00000001645
• Aliases: None
• Description: None

Sequence

>retro_nleu_350
ATGGCTAACAACAGCCCCGCGCTGACAGGCAACTCACAGCTGCAGCACCAGACGGCCGCTGCTGCGGCTCAGCAACAGCA
GCAGTGCGGCGGCGGCGGCGGCGTAGCGCCGGCGGTCTGCGGCAAGCAGGGCAATGTGCTCCCTCTCCGGGGCGACGAGA
AGACCATGAACTTCAACCCCATGATCCTGACCAACATCCTGTCATTGCCTTGCTTCAAAATACAGCTCTACGAGCTCAAG
ACCTACCACGAGGTGGTGGACGAGATCTACTTTAAGGTCACGCACGTTGAACCATGGGAGAAAGGAAGCAGGAAAACAGC
TGGCCAGACAGGGATGTGCGGAGGGGTAAGTAGAAGTTCGAGGTGTTGGAACAGGAGGAATTGTTTCTACAGCATTTTGC
CTGTTATACAAATTATTTACCCTAAAGTTAACTCGAAAGCAAGTGATGGGTCTTATAACACACACAGACTCTCCATATAT
TAGAGCGCTTGGATTTATGTATATCAGATATACACAGCCCCCTAAAGATCTATGGGACTGGTTTGAATCCTTCCTTGATG
ATGAAGAGGACCTAGATGTGAAGGCTGGTGGAGGCTGTGTAATGACCATTGGAGAAATGCTACGATCTTTTCTCACAAAA
CTGGAGTGGTTTTCTACCTTGTTTCCAAGAATTCCAGTTCCAGTTCAAAAGAATATTGATCAACAGATTAAAACCCGACC
TAGAAAAATCAAGAAAGATGGGGAGGAAGGTGCTGAGGAAATAGACAGACATGTTGAATGCAGACGTTCAAGGTCTCCAA
GGAGATCTCTGAGTCCACGGAGGTCCCCAAGAAGATCAAGAAGTAGAAGTCATCATCGGGAGGGCCATGGGTCTTCTAGT
TTTGACAGAGAATTAGAAAGAGAGAAAGAACGCCAGCGACTAGAGCGTGAAGCCAAAGAAAGGGAGAAAGAACGGCGAAG
ATCCCGAAGTATTGACCGGGGGTTGGAACGTAGGTGCAGCAGAAGTAGGGAAAGGCATAGAAGTCACAGTCGAAGTCGTG
ATAGGAAAGGGGATAGAAGGGACAGGGATCGAGAAAGAGAGAAGGAAAATGAGAGAGGTAGAAGACGAGATCGTGACTAT
GATAAGGAAAGAGGAAATGAACGAGAAAAA

Alignment

ORF - retro_nleu_350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.61 %
• Parental protein coverage: 69.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MANNSPALTGNSQPQHQTAAAAAQQQQQCGGGGGATKPAVSGKQGNVLPLWGNEKTMNLNPMILTNILSS
          MANNSPALTGNSQ.QHQTAAAAAQQ.QQ...............QGNVLPL.G.EKTMN.NPMILTNILS.
Retrocopy MANNSPALTGNSQLQHQTAAAAAQQ-QQQXXXXXXXXXXXXXXQGNVLPLRGDEKTMNFNPMILTNILSL

Parental  PYFKVQLYELKTYHEVVDEIYFKVTHVEPWEKGSR-KTAGQTGMCGG---VRGVGTGGIVSTAFCLLYKL
          P.FK.QLYELKTYHEVVDEIYFKVTHVEPWEKGSR.K.....G...G...VRGVGTGGIVSTAFCLLYKL
Retrocopy PCFKIQLYELKTYHEVVDEIYFKVTHVEPWEKGSR>KQLARQGCAEG*VEVRGVGTGGIVSTAFCLLYKL

Parental  FTLKLTRKQVMGLITHTDSPYIRALGFMYIRYTQPPTDLWDWFESFLDDEEDLDVKAGGGCVMTIGEMLR
          FTLKLTRKQVMGLITHTDSPYIRALGFMYIRYTQPP.DLWDWFESFLDDEEDLDVKAGGGCVMTIGEMLR
Retrocopy FTLKLTRKQVMGLITHTDSPYIRALGFMYIRYTQPPKDLWDWFESFLDDEEDLDVKAGGGCVMTIGEMLR

Parental  SFLTKLEWFSTLFPRIPVPVQKNIDQQIKTRPRKIKKDGKEGAEEIDRHVERRRSRSPRRSLSPRRSPRR
          SFLTKLEWFSTLFPRIPVPVQKNIDQQIKTRPRKIKKDG.EGAEEIDRHVE.RRSRSPRRSLSPRRSPRR
Retrocopy SFLTKLEWFSTLFPRIPVPVQKNIDQQIKTRPRKIKKDGEEGAEEIDRHVECRRSRSPRRSLSPRRSPRR

Parental  SRSRSHHREGHGSSSFDRELEREKERQRLEREAKEREKERRRSRSIDRGLERRRSRSRERHRSRSRSRDR
          SRSRSHHREGHGSSSFDRELEREKERQRLEREAKEREKERRRSRSIDRGLERR.SRSRERHRS.SRSRDR
Retrocopy SRSRSHHREGHGSSSFDRELEREKERQRLEREAKEREKERRRSRSIDRGLERRCSRSRERHRSHSRSRDR

Parental  KGDRRDRDREREKENERGRRRDRDYDKERGNEREK
          KGDRRDRDREREKENERGRRRDRDYDKERGNEREK
Retrocopy KGDRRDRDREREKENERGRRRDRDYDKERGNEREK

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_350 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002510	1 retrocopy	retro_cjac_3189,
Nomascus leucogenys	ENSNLEG00000001645	1 retrocopy	retro_nleu_350 ,
Tursiops truncatus	ENSTTRG00000006479	1 retrocopy	retro_ttru_236,