RetrogeneDB ID: retro_cjac_1603

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:55800876..55802196(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1B
• Ensembl ID: ENSCJAG00000020874
• Aliases: None
• Description: tubulin, alpha 1b [Source:HGNC Symbol;Acc:18809]

Sequence

>retro_cjac_1603
ATGCATGAGTGCATCTCCATCCATGTTGGCCAGTCTGGTGTCCAGATTGGCAATGCCTGCTGGGAGCTCTACTGCCTGGA
ACATGGCATCCAGCCCGATGGCCAGATGCCAAGTGACAAGACTATTGGGGGAGGAGATGACTCCTTCAACACCTTCTTCA
GTGAGATGGGCGCTGGCAAGCACGTGCCCTGGGCAGTGTTTGTAGACCTGGAACCCAAGGTCATTGATGAAATTCACACT
GGCACCCACCGCCAGCTCTTCCATCCTGAGCAGCTTGTCACAGGCAAGGAAGATGCTGCCAATAACTATGCCCGAGGGCA
CTACACCATCGGCAAGATCATTGACCTTGTGCTGGACTGAATTCATAAATTGGCTGACCAGTGCACCGGTCTCCAGGGCT
TCTTGGTTTTCCACAGCTTTGGTGGGGGAACTGGTTCTGGGTTCACCTCCCTGCTCATGGAATGGCTCTCAGTTGATTAT
GGCAATAAGTCCAAGCTGGAGTTCTCCATCTACCCAGCGCCCCAGGTTTCCACAGCTGTAGTTGAGCCCTACAGTTCCAT
CCTCACCACCCACACCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACAATGAGGTCATCTATGACGTCTGTCGTA
GAAACCTCGATATCGAGTGCCCAACCTACACTAACCTGAATAGATTAATAGATCAAATTGTGTCCTCCATCACTGCTTCC
CTGAGATTCGATGGAGCCCTGAATGTTGACCTGACAGAATTCCAGACCAACCTGGTGCCCTATCCTCGCATCCACTTCCC
TCTGGCCACATATGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAACAGCTTTCAGTAGCAGAGATCACCAACGCTT
GCTTTGAGCCAGCCAACCAGATGATGAAATGTGACCCTCGCCATGGTAAACACATGGCTTGCTGCCTGTTGTGCCGTGGT
GATGTGGTTACCAAAGATGTCAGTGCTGCCGTCGCCACCATCAAGACCAAGCGCAGCATCCAGTTTGTGGATTGGTGCCC
TACTGGTTTCAAGGTTGGCATCAACTACCAGCCTCCCTCTGTGGTACCTGGTGGATACCTGGCCAAGGTACAGAGAGCTG
TGTGCATCCTGAGCAACACCACAGCCATTGCTGAGGCCTGGGCTCGCCTGGACCACAAGTTTGACCTGATGTATACCGCG
CATGCCTTTGTTCACTGGTACGTGGGTGAGGGGATGGAGGAAGGAGAGTTTTCAGAGGCCCGTGAGGACATGGCTGCCCT
TGAGAAGGATTATGAGGAGGTTGGTGTGGATTCTGTTGAA

Alignment

ORF - retro_cjac_1603 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.97 %
• Parental protein coverage: 97.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
          M.ECISIHVGQ.GVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSE.GAGKHVP.AVFVDL
Retrocopy MHECISIHVGQSGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSEMGAGKHVPWAVFVDL

Parental  EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHS
          EP.VIDE..TGT.RQLFHPEQL.TGKEDAANNYARGHYTIGK.IIDLVLD.I.KLADQCTGLQGFLVFHS
Retrocopy EPKVIDEIHTGTHRQLFHPEQLVTGKEDAANNYARGHYTIGK-IIDLVLD*IHKLADQCTGLQGFLVFHS

Parental  FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY
          FGGGTGSGFTSLLME.LSVDYG.KSKLEFSIYPAPQVSTAVVEPY.SILTTHTTLEHSDCAFMVDNE.IY
Retrocopy FGGGTGSGFTSLLMEWLSVDYGNKSKLEFSIYPAPQVSTAVVEPYSSILTTHTTLEHSDCAFMVDNEVIY

Parental  DICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK
          D.CRRNLDIE.PTYTNLNRLI.QIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK
Retrocopy DVCRRNLDIECPTYTNLNRLIDQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK

Parental  AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTG
          AYHEQLSVAEITNACFEPANQM.KCDPRHGK.MACCLL.RGDVV.KDV.AA.ATIKTKRSIQFVDWCPTG
Retrocopy AYHEQLSVAEITNACFEPANQMMKCDPRHGKHMACCLLCRGDVVTKDVSAAVATIKTKRSIQFVDWCPTG

Parental  FKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
          FKVGINYQPP.VVPGG.LAKVQRAVC.LSNTTAIAEAWARLDHKFDLMY...AFVHWYVGEGMEEGEFSE
Retrocopy FKVGINYQPPSVVPGGYLAKVQRAVCILSNTTAIAEAWARLDHKFDLMYTAHAFVHWYVGEGMEEGEFSE

Parental  AREDMAALEKDYEEVGVDSVE
          AREDMAALEKDYEEVGVDSVE
Retrocopy AREDMAALEKDYEEVGVDSVE

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	127.13 RPM
SRP051959_heart	0.02 RPM	89.60 RPM
SRP051959_kidney	0.04 RPM	55.67 RPM
SRP051959_liver	0.00 RPM	43.93 RPM
SRP051959_lung	0.02 RPM	84.92 RPM
SRP051959_lymph_node	0.00 RPM	68.26 RPM
SRP051959_skeletal_muscle	0.00 RPM	29.35 RPM
SRP051959_spleen	0.00 RPM	80.69 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1603 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1603 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1603 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012244	1 retrocopy	retro_btau_402,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Callithrix jacchus	ENSCJAG00000020874	2 retrocopies	retro_cjac_1603 , retro_cjac_1861,
Callithrix jacchus	ENSCJAG00000020894	2 retrocopies	retro_cjac_1209, retro_cjac_3157,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Homo sapiens	ENSG00000123416	1 retrocopy	retro_hsap_808,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Macropus eugenii	ENSMEUG00000011167	4 retrocopies	retro_meug_1121, retro_meug_157, retro_meug_1616, retro_meug_1964,
Monodelphis domestica	ENSMODG00000015206	2 retrocopies	retro_mdom_1632, retro_mdom_348,
Mus musculus	ENSMUSG00000023004	6 retrocopies	retro_mmus_1562, retro_mmus_1607, retro_mmus_1742, retro_mmus_1987, retro_mmus_3297, retro_mmus_3327,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pan troglodytes	ENSPTRG00000012950	1 retrocopy	retro_ptro_2158,
Sus scrofa	ENSSSCG00000000190	2 retrocopies	retro_sscr_380, retro_sscr_702,