RetrogeneDB ID: retro_cjac_423

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:77190330..77191011(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHTOP
• Ensembl ID: ENSCJAG00000010383
• Aliases: None
• Description: chromatin target of PRMT1 [Source:HGNC Symbol;Acc:24511]

Sequence

>retro_cjac_423
TTTACTAATATGCTGAAGAACAAACAGCCGACGCCAGTGAATATTCGGGCTTCGATGCAGCAACAACAGCAGCTAGCCAG
TGCCAGAAACAGAAGACTGGCCCAGCAGATGGAGAATAGACCCTCTGTCCAGGTGGCATTAAAGCTTAAGCAGAAGAGCT
TAAAGCAGCGCCTGGGTAAGAGTAACATCCAGGCACGGTTAGGCCGACCCATAGGGGCCCTGGCCAGGGGAGCAATTGGA
GGACGAGACCTACCCATAATCCAGAGAGGCTTACTCAGAGGAGGACTACGTGGGGGACGTGCCACCAGAACCCTGCTTAG
GGGCAGGATGTCACTCCGAGGCCAAAACCTGCTCCAAGGTGGATGAGCCGTAGCTCCCCGAATGGGCTTAAGAAGAGGTG
GTGTTCGAGGTCATGGAGGTCCTGGGAGAGGGGTCCTAGGACGTGGAGCTATGGGTCGTGGCGGAATCGGTGGTAAAGGT
CGGGGTATGATAGGTCGGGGAAGAGGGGGCTTTGGAGGCTGAGGCCGAGACCATGGACGAGGGAGAGGTGCCCTTGCTCG
CCCTGTATTGACCAAGGAGCAGCTGAACAACCAATTGGATGCATACATGTCGAAAACAAAAGGACACCTGGATGCTGAGT
TGGATGCCTACATGGCGCAGACAGATCCCGAAACCAATGAT

Alignment

ORF - retro_cjac_423 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.63 %
• Parental protein coverage: 91.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FTNMLKNKQPTPVNIRASMQQQQQLASARNRRLAQQMENRPSVQAALKLKQKSLKQRLGKSNIQARLGRP
          FTNMLKNKQPTPVNIRASMQQQQQLASARNRRLAQQMENRPSVQ.ALKLKQKSLKQRLGKSNIQARLGRP
Retrocopy FTNMLKNKQPTPVNIRASMQQQQQLASARNRRLAQQMENRPSVQVALKLKQKSLKQRLGKSNIQARLGRP

Parental  IGALARGAIGGRGLPIIQRGLPRGGLRGGRATRTLLRGGMSLRGQNLLRGGRAVAPRMGLRRGGVRGRGG
          IGALARGAIGGR.LPIIQRGL.RGGLRGGRATRTLLRG.MSLRGQNLL.GG.AVAPRMGLRRGGVRG.GG
Retrocopy IGALARGAIGGRDLPIIQRGLLRGGLRGGRATRTLLRGRMSLRGQNLLQGG*AVAPRMGLRRGGVRGHGG

Parental  PGRGGLGRGAMGRGGIGGRGRGMIGRGKGGFGGRGRGRGRGRGALARPVLTKEQLDNQLST--CKTKGHL
          PGRG.LGRGAMGRGGIGG.GRGMIGRG.GGFGG.GR..GRGRGALARPVLTKEQL.NQL.....KTKGHL
Retrocopy PGRGVLGRGAMGRGGIGGKGRGMIGRGRGGFGG*GRDHGRGRGALARPVLTKEQLNNQLDAYMSKTKGHL

Parental  DAELDAYMAQTDPETND
          DAELDAYMAQTDPETND
Retrocopy DAELDAYMAQTDPETND

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	1.62 RPM	20.21 RPM
SRP051959_heart	2.46 RPM	24.05 RPM
SRP051959_kidney	2.40 RPM	25.45 RPM
SRP051959_liver	1.43 RPM	15.77 RPM
SRP051959_lung	3.11 RPM	29.33 RPM
SRP051959_lymph_node	2.97 RPM	33.93 RPM
SRP051959_skeletal_muscle	2.64 RPM	26.38 RPM
SRP051959_spleen	2.50 RPM	27.33 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_423 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_423 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_423 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013518	1 retrocopy	retro_chof_6,
Callithrix jacchus	ENSCJAG00000010383	3 retrocopies	retro_cjac_2059, retro_cjac_423 , retro_cjac_431,
Felis catus	ENSFCAG00000002740	1 retrocopy	retro_fcat_1925,
Myotis lucifugus	ENSMLUG00000016098	2 retrocopies	retro_mluc_201, retro_mluc_247,
Mus musculus	ENSMUSG00000001017	2 retrocopies	retro_mmus_1693, retro_mmus_1852,
Rattus norvegicus	ENSRNOG00000012760	1 retrocopy	retro_rnor_1095,
Ictidomys tridecemlineatus	ENSSTOG00000000660	1 retrocopy	retro_itri_1169,
Tupaia belangeri	ENSTBEG00000012442	1 retrocopy	retro_tbel_293,
Vicugna pacos	ENSVPAG00000010259	1 retrocopy	retro_vpac_353,