RetrogeneDB ID: retro_nleu_3024

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397590.1:76221..77311(+)
• Located in intron of: ENSNLEG00000000397

Retrocopy information

• Ensembl ID: ENSNLEG00000000449
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PA2G4
• Ensembl ID: ENSNLEG00000017544
• Aliases: None
• Description: None

Sequence

>retro_nleu_3024
ATGTCAGGCAAAGACGAGCAGCAGGAGCAAACTATCGCCGAGGACCTGGTCGTGACCAAGTATAAGATGGGGCGCGACAT
TGCCAACGGGATACTTCGGTCCTTGGTGGACGCATCTAGCTCAGGTGTGTCAGTACTGAGCCTGTGTGAGAAAGGTGATG
CCATGATTATGCAAGAAACTGGGAAAATCTTCAAGAAAGAAAAAGAGATGAAGAGAGGTATTGCTTTTCCCACCAGCATT
TCGGTAAATAACTGTGTATGTCACTTCTCCCCTTTGAAGAGAGACCAGGATTACATTCTCAAGGAAGGTGACTTGGTAAA
AATTGACCTTGGGGTCCATGTGGATGGCTTCATCACTAATGTAGCTCATACTTTTGTGGCTGATGTAGCTCAGGAGACCC
AGGTAACAGGAAGGAAAGCAGATGTTATTAAGGCAGCTCACCTTTGTGCTGAAGCTGCCCTACGCCTGGTCACACCTGGA
AATCAGAACACACAAGTGACAGAAGCCTGGAACAAAGTTGCCCACTCATTTAACTGCACGCCAATAGAAGGTATGCCTGT
CACACCAGCTGAAGCAGCATGTCATCGATGGAGAAAAAACCATTACCCAGAATCCCACAGACCAGCAGAAGAAGGACCAT
GAAAAAGCTGAATTTGAGGTACATGAAGTATATGCTGTGGATGTTCTCGTCAGCTTAGGAGAGGGCAAGGCCAAGGATGC
AGGAGAGAGAACCACTATTTACAAACGAGACCCCTCCAAACAGTATGGACTGAAAATGAAAACTTGACGTGCCTTCCTCA
GTGAGATGAAAAGATGTTTTGATGCCATGCCGTTTACTTTAAGAGCATGAGAAGATGAGAAGAAGGCTCAGATGGGTGTG
GTGGAGTGTGCCAAACATGAACTGCTGCAACCATTTAATGTTCTCTATGAGAAGGAGGGTGAATTTGTTGCCCAGTTTAA
ATTTACAGTTCTGCTCATGCCCAGTGGCCCCATGTGGATAACCAGTGGTCCCTTCCAGCCTGACCTCTATAAATCTGAGA
TGGAGGTCCAGGATGCAGAGGTAAAGACCCTCCTCCAGAGTTCTGCAAGT

Alignment

ORF - retro_nleu_3024 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.76 %
• Parental protein coverage: 92.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGEDEQQEQTIAEDLVVTKYKMGGDIANRVLRSLVEASSSGVSVLSLCEKGDAMIMEETGKIFKKEKEM
          MSG.DEQQEQTIAEDLVVTKYKMG.DIAN..LRSLV.ASSSGVSVLSLCEKGDAMIM.ETGKIFKKEKEM
Retrocopy MSGKDEQQEQTIAEDLVVTKYKMGRDIANGILRSLVDASSSGVSVLSLCEKGDAMIMQETGKIFKKEKEM

Parental  KKGIAFPTSISVNNCVCHFSPLKSDQDYILKEGDLVKIDLGVHVDGFIANVAHTFVVDVAQGTQVTGRKA
          K.GIAFPTSISVNNCVCHFSPLK.DQDYILKEGDLVKIDLGVHVDGFI.NVAHTFV.DVAQ.TQVTGRKA
Retrocopy KRGIAFPTSISVNNCVCHFSPLKRDQDYILKEGDLVKIDLGVHVDGFITNVAHTFVADVAQETQVTGRKA

Parental  DVIKAAHLCAEAALRLVKPGNQNTQVTEAW-QVAHSFNCTPIEGM-LSHQLKQHVIDGEKTIIQNPTDQQ
          DVIKAAHLCAEAALRLV.PGNQNTQVTEAW..VAHSFNCTPIEGM.LSHQLKQHVIDGEKTI.QNPTDQQ
Retrocopy DVIKAAHLCAEAALRLVTPGNQNTQVTEAWNKVAHSFNCTPIEGM>LSHQLKQHVIDGEKTITQNPTDQQ

Parental  KKDHEKAEFEVHEVYAVDVLVSSGEGKAKDAGQRTTIYKRDPSKQYGLKMKTSRAFFSEVERRFDAMPFT
          KKDHEKAEFEVHEVYAVDVLVS.GEGKAKDAG.RTTIYKRDPSKQYGLKMKT.RAF.SE..R.FDAMPFT
Retrocopy KKDHEKAEFEVHEVYAVDVLVSLGEGKAKDAGERTTIYKRDPSKQYGLKMKT*RAFLSEMKRCFDAMPFT

Parental  LRAFEDEKKARMGVVECAKHELLQPFNVLYEKEGEFVAQFKFTVLLMPNGPMRITSGPFEPDLYKSEMEV
          LRA.EDEKKA.MGVVECAKHELLQPFNVLYEKEGEFVAQFKFTVLLMP.GPM.ITSGPF.PDLYKSEMEV
Retrocopy LRA*EDEKKAQMGVVECAKHELLQPFNVLYEKEGEFVAQFKFTVLLMPSGPMWITSGPFQPDLYKSEMEV

Parental  QDAELKALLQSSAS
          QDAE.K.LLQSSAS
Retrocopy QDAEVKTLLQSSAS

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_3024 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 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007181	2 retrocopies	retro_chof_1089, retro_chof_1847,
Homo sapiens	ENSG00000170515	6 retrocopies	retro_hsap_1930, retro_hsap_2413, retro_hsap_2868, retro_hsap_3646, retro_hsap_4191, retro_hsap_4895,
Macaca mulatta	ENSMMUG00000002164	2 retrocopies	retro_mmul_1168, retro_mmul_2631,
Nomascus leucogenys	ENSNLEG00000017544	6 retrocopies	retro_nleu_1212, retro_nleu_1260, retro_nleu_163, retro_nleu_3024 , retro_nleu_506, retro_nleu_612,
Pongo abelii	ENSPPYG00000025851	7 retrocopies	retro_pabe_1595, retro_pabe_1778, retro_pabe_2375, retro_pabe_2869, retro_pabe_2993, retro_pabe_3430, retro_pabe_3807,
Sus scrofa	ENSSSCG00000000377	1 retrocopy	retro_sscr_338,
Sus scrofa	ENSSSCG00000022666	2 retrocopies	retro_sscr_1143, retro_sscr_337,
Vicugna pacos	ENSVPAG00000009523	1 retrocopy	retro_vpac_2,