RetrogeneDB ID: retro_cjac_1209

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:54221532..54222885(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1A
• Ensembl ID: ENSCJAG00000020894
• Aliases: None
• Description: None

Sequence

>retro_cjac_1209
ATGCGTGAGTGCATCTCCATCCATGTTGGCCAGGCTTGTGTCCAGATTGGCAATGACTGCTGGGAGCTCTACTGCCTGGA
ACATGGCATTCAGCCCGATGGCCAGATGCCAAGTGACAAGACCATTGGGGGAGGAGATGACTCCTTCAACACCTTCTTCA
GTGAGACGGGTGCTGGCAAGCACGTGCCCCGGGCAGTGTTTGTAGACCTGGAACCCACGGTCATTGATGAAGTTCGCACT
GGCACCTACCGCCAGCTCTTCCACCCTGAACAGCTCATCACAGGCAAGGAAGATGATGCCAATAACTATGCCCGAGGGCA
CTACACCATCGGCAAGGAGATCATTGACCTTGTGTTGGACTGAATTCGTAAACTGGCTGACCAGTGCACCGGTCTCCAGG
GCTTCTTGGTTTTCCACAGCTTTGGTGGGAGAACTGGTTCTGGGTTCACCTCCCTGCTCATGGAACGGCTCTCAGTTGAT
TATGGCAAGAAGTCCAAGCTGGAGTTCTCCATCTACCCGGCGCCCCAGGTTTCCACAGCTGTAGTTGAGCCCTACAACTC
CATCCTCACCACCCACTCCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACAATGAGGCCATCTATGACATCTGTC
GTAGAAACCTCGATATTGAGCGCCCAACCTACACTAACCTGAATAGATTAATAGGTCAAATTGTGTCCTCCATCACTGCT
TCCCTGAGATTTGATGGAGCCCTGAATGTTGACCTGACAGAATTCCAGACCAACCTGGTGCCCTATCCTCGCATCCACTT
CCCTCTGGCCACATATGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAACAGCTTTCTGTAGCAGAGATCACCAATG
CTTGCTTTGAGCCAGCCAACCAGATGGTGAAATGTGACCCTCGCCATGGTAAATACATGGCTTGCTGCCTGTTGTACTGT
GGTGACGTGGTTCCCAAAGATGTCAATGCTGCCATCGCCACCATCAAGACCAAGCGTACCATCCAGTTTGTGGATTGGTG
CCCCACTGGCTTCAAGGTTGGCATCAACTACCAGCCTCCCACTGTGGTGCCTGGTGGAGACCTGGCCAAGGTACAGAGAG
CTGTGTGCATGCTGAGCAACACCACAGCCATTGCTGAGGCCTGGGCTCACCTGGACCACAAGTTTGACCTGATGTATGCC
AAGCGTGCCTTTGTTCACTGGTACGTGGGTGAGGGGATGGAGGAAGGAGAGTTTTCAGAGGCCCGTGAGGACATGGCTGC
CCTTGAGAAGGATTATGAGGAGGTTGGTGTGGATTCTGTTGAAGGAGAAGGCGAGGAAGAAGGTGAGGAATAC

Alignment

ORF - retro_cjac_1209 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.45 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
          MRECISIHVGQA.VQIGN.CWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
Retrocopy MRECISIHVGQACVQIGNDCWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL

Parental  EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHS
          EPTVIDEVRTGTYRQLFHPEQLITGKED.ANNYARGHYTIGKEIIDLVLD.IRKLADQCTGLQGFLVFHS
Retrocopy EPTVIDEVRTGTYRQLFHPEQLITGKEDDANNYARGHYTIGKEIIDLVLD*IRKLADQCTGLQGFLVFHS

Parental  FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY
          FGG.TGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTH.TLEHSDCAFMVDNEAIY
Retrocopy FGGRTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHSTLEHSDCAFMVDNEAIY

Parental  DICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK
          DICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK
Retrocopy DICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK

Parental  AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYCGDVVPKDVNAAIATIKTKRTIQFVDWCPTG
          AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYCGDVVPKDVNAAIATIKTKRTIQFVDWCPTG
Retrocopy AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYCGDVVPKDVNAAIATIKTKRTIQFVDWCPTG

Parental  FKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
          FKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWA.LDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
Retrocopy FKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWAHLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE

Parental  AREDMAALEKDYEEVGVDSVEGEGEEEGEEY
          AREDMAALEKDYEEVGVDSVEGEGEEEGEEY
Retrocopy AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.02 RPM	4.08 RPM
SRP051959_heart	0.04 RPM	4.67 RPM
SRP051959_kidney	0.00 RPM	2.17 RPM
SRP051959_liver	0.02 RPM	0.87 RPM
SRP051959_lung	0.07 RPM	5.61 RPM
SRP051959_lymph_node	0.02 RPM	3.42 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.36 RPM
SRP051959_spleen	0.02 RPM	4.12 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1209 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1209 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1209 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001489	3 retrocopies	retro_btau_251, retro_btau_350, retro_btau_929,
Callithrix jacchus	ENSCJAG00000020874	2 retrocopies	retro_cjac_1603, retro_cjac_1861,
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,