RetrogeneDB ID: retro_nleu_245

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397262.1:23036090..23037440(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1A
• Ensembl ID: ENSNLEG00000017836
• Aliases: None
• Description: None

Sequence

>retro_nleu_245
ATGCGTGAGTGCATCTCCATCCACGTTGGCCAGGCTGGTGTCCAGATTGGCATTGCCTGCTGGGAGCTCTACTGCCTGGA
ACACGGCATCCAACCTGATGGCCAGATGCCAAGTGACAAGACCGTTGGGGGAGGAGATGTCTCCTTCAACACCTTCAGTG
AGATGGGCGCTGGCAAGCACGTGCCCCGGGCTGTGTTTGTAGACTTGGAACCCATGGTCATTGATGAAGTTCGCACTGGC
ACCTACCGCCAGCTCTTCCACCCTGAGCAGCTCATCACAGGCAAGGAAGATGCTGCCAATAACTATGCCCGAGGGCACTA
CACCATTGGCAAGGAGATCATTGACCTTGTGTTGGACCAAACTCACAAGCTGGCTGACCAGTGCACCGGTCTTCAGGGCT
TCTTGGTTTTCCACAGCTTTGGTGGGGGAACTGGTTCTAGGTTCGCCTCCCTGCTCATGAAATGTCTCTCAGTTGATTAT
GGCAAGAAGTCCAAGCTGGAGTTCTCCATTTACCTGGTGCCCCAGGTTTCCACAGCTGTAGTTGAGCTCTACAACTCCAT
CCTCACCACCCACACCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACAATGAGGCCATCTATGACATCTGTCGTA
GAAACCTCGATATCGAGCGCCCAACCTAAACTAACCTTAACCGCCTTATTAGCCAGATTGTGTCCTCCATCACGGCTTCC
CTGAGATTTGATGGAGCCCTGAATGTTGACCTGACAGAATTTCAGACCAACCTGGTGCCCTACCCCTGCATCCACTTCCC
TCTGGCCACATACGCCCCTGTCATCTCCGCTGAGAAAGCCTACCATGAACAGCTTTCTGTAGCAGAGATCACCAATGCTT
GCTTTGAGCCAGCCAACCAGATGGTGAAATGTGACCCTCGCCATGGAAAATACATGGCTTGCTGCCTATTGTACTATGGT
GATGTGGTTCCCAAAGATGTCAATGCTGCCATTGCCATCATCAAGACCAAGTGCAGCATCAAGTTTGTAGATTGGTGCCC
CACTGGCTTCAGGGTTGGCATCAACTACCAGCCTCCCACTGTGGTGCCTGGTGGAGACCTGGCCAAGGTACAGAGAGCTG
TGTGCATGCTGAGCAACACCACAGCCATTGCTGAGGCCTGGGCTCACCTGGACCACAAGTTTGACCTGATGTATGCCAAG
CGTGCCTTTGTTCACTGGTACGTGGGTGAGGGGATGGAGGAAGGCGAGTTTTCAGAGGCCCGTGAAGACATGGCTGCCCT
TGAGAAGGATTATGAGGAGGTTGGTGTGGATTCTGTTGAAGGAGAGGGTGAGGAAGAAGGAGAGGAATAC

Alignment

ORF - retro_nleu_245 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.24 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
          MRECISIHVGQAGVQIG.ACWELYCLEHGIQPDGQMPSDKT.GGGD.SFNTF.SE.GAGKHVPRAVFVDL
Retrocopy MRECISIHVGQAGVQIGIACWELYCLEHGIQPDGQMPSDKTVGGGDVSFNTF-SEMGAGKHVPRAVFVDL

Parental  EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHS
          EP.VIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD...KLADQCTGLQGFLVFHS
Retrocopy EPMVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDQTHKLADQCTGLQGFLVFHS

Parental  FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY
          FGGGTGS.F.SLLM..LSVDYGKKSKLEFSIY..PQVSTAVVE.YNSILTTHTTLEHSDCAFMVDNEAIY
Retrocopy FGGGTGSRFASLLMKCLSVDYGKKSKLEFSIYLVPQVSTAVVELYNSILTTHTTLEHSDCAFMVDNEAIY

Parental  DICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK
          DICRRNLDIERPT.TNLNRLI.QIVSSITASLRFDGALNVDLTEFQTNLVPYP.IHFPLATYAPVISAEK
Retrocopy DICRRNLDIERPT*TNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPCIHFPLATYAPVISAEK

Parental  AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTG
          AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLY.GDVVPKDVNAAIA.IKTK..I.FVDWCPTG
Retrocopy AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYYGDVVPKDVNAAIAIIKTKCSIKFVDWCPTG

Parental  FKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
          F.VGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWA.LDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
Retrocopy FRVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWAHLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE

Parental  AREDMAALEKDYEEVGVDSVEGEGEEEGEEY
          AREDMAALEKDYEEVGVDSVEGEGEEEGEEY
Retrocopy AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

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_245 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 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001489	3 retrocopies	retro_btau_251, retro_btau_350, retro_btau_929,
Callithrix jacchus	ENSCJAG00000020894	2 retrocopies	retro_cjac_1209, retro_cjac_3157,
Dasypus novemcinctus	ENSDNOG00000004121	1 retrocopy	retro_dnov_43,
Equus caballus	ENSECAG00000013798	1 retrocopy	retro_ecab_223,
Homo sapiens	ENSG00000167552	1 retrocopy	retro_hsap_3313,
Nomascus leucogenys	ENSNLEG00000017836	2 retrocopies	retro_nleu_245 , retro_nleu_2757,
Oryctolagus cuniculus	ENSOCUG00000027812	1 retrocopy	retro_ocun_197,
Pteropus vampyrus	ENSPVAG00000004645	2 retrocopies	retro_pvam_1283, retro_pvam_414,
Rattus norvegicus	ENSRNOG00000004559	3 retrocopies	retro_rnor_1200, retro_rnor_2006, retro_rnor_446,
Vicugna pacos	ENSVPAG00000005749	4 retrocopies	retro_vpac_157, retro_vpac_210, retro_vpac_429, retro_vpac_72,