RetrogeneDB ID: retro_cjac_373

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:136749047..136749944(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023347
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000005125
• Aliases: None
• Description: None

Sequence

>retro_cjac_373
ATGACAGATGCCGCTGTGTCCTTCGCCAAGGACTTCCTGGCAGGTGGAGTGGCCGCAGCCATCTCCAAGACGGCGGTAGC
GCCCATCGAGCGGGTCAAGCTGCTGCTGCAGGTACAGCATGCCAGCAAGCAGATCACTGCAGATAAGCAATACAAGGGTA
TTATAGACTGCGTGGTCCGTATTCCCAAGGAGCAGGGAGTCCTGTCCTTCTGGCTCGGTAACCTGGCTAATGTCATCAGA
TACTTCCCCACCCAGGCCCTTAACTTCGCCTTCAAAGATAAATACAAGCAGATCTTCCTGGGTGGTGTGGACAAGAGGAC
CCAGTTTTGGCGCTACTTTGCAGGGAATCTGGCATCAGGCGGTGCTGCTGGGGCCACATCCTTGTGTTTTGTGTACCCTC
TTGATTTTGCCCGTACCCGTCTAGCAGCAGATGTGGGTAAAGCTGGAGCTGAAAGGGAATTCCGAGGCCTCGGCGACTGC
CTGGTTAAGATCTACAAATCTGATGGGATTAAGGGCCTGTACCAAGGCTTTAATGTGTCTGTGCAGGGTATTATCATCTA
CCGAGCTGCCTACTTCGGTATCTATGACACTGCAAAGGGAATGCTTCCAGATCCCAAGAACACTCACATCGTTATCAGCT
GGATGATCGCACAGACTGTCACTGCTGTTGCTGGGTTGACTTCCTATCCATTTGACACTGTTCGCCGCCGCATGATGATG
CAGTCGGGGCGCAAAGGAACTGACATCATGTACACAGGCACACTTGACTGCTGGAGGAAGATTGCTCATGATGAAGGAGG
CAAAGCTTTCTTCAAGGGTGCATGGTCCAATGTTCTCCGAGGCATGGGTGGTGCTTTTGTACTTGTCTTGTATGATGAAA
TCAAGAAGTACACATAA

Alignment

ORF - retro_cjac_373 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTDAAVSFAKDFLAGGVAAAISKTAVAPIERVKLLLQVQHASKQITADKQYKGIIDCVVRIPKEQGVLSF
          MTDAAVSFAKDFLAGGVAAAISKTAVAPIERVKLLLQVQHASKQITADKQYKGIIDCVVRIPKEQGVLSF
Retrocopy MTDAAVSFAKDFLAGGVAAAISKTAVAPIERVKLLLQVQHASKQITADKQYKGIIDCVVRIPKEQGVLSF

Parental  WRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDKRTQFWRYFAGNLASGGAAGATSLCFVYPLDFARTR
          W.GNLANVIRYFPTQALNFAFKDKYKQIFLGGVDKRTQFWRYFAGNLASGGAAGATSLCFVYPLDFARTR
Retrocopy WLGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDKRTQFWRYFAGNLASGGAAGATSLCFVYPLDFARTR

Parental  LAADVGKAGAEREFRGLGDCLVKIYKSDGIKGLYQGFNVSVQGIIIYRAAYFGIYDTAKGMLPDPKNTHI
          LAADVGKAGAEREFRGLGDCLVKIYKSDGIKGLYQGFNVSVQGIIIYRAAYFGIYDTAKGMLPDPKNTHI
Retrocopy LAADVGKAGAEREFRGLGDCLVKIYKSDGIKGLYQGFNVSVQGIIIYRAAYFGIYDTAKGMLPDPKNTHI

Parental  VISWMIAQTVTAVAGLTSYPFDTVRRRMMMQSGRKGTDIMYTGTLDCWRKIARDEGGKAFFKGAWSNVLR
          VISWMIAQTVTAVAGLTSYPFDTVRRRMMMQSGRKGTDIMYTGTLDCWRKIA.DEGGKAFFKGAWSNVLR
Retrocopy VISWMIAQTVTAVAGLTSYPFDTVRRRMMMQSGRKGTDIMYTGTLDCWRKIAHDEGGKAFFKGAWSNVLR

Parental  GMGGAFVLVLYDEIKKYT
          GMGGAFVLVLYDEIKKYT
Retrocopy GMGGAFVLVLYDEIKKYT

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	0.07 RPM	44.86 RPM
SRP051959_heart	0.11 RPM	11.49 RPM
SRP051959_kidney	0.09 RPM	66.07 RPM
SRP051959_liver	0.09 RPM	74.64 RPM
SRP051959_lung	0.05 RPM	16.63 RPM
SRP051959_lymph_node	0.05 RPM	20.18 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.65 RPM
SRP051959_spleen	0.00 RPM	21.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_cjac_373 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
HX536901	136749571	136749772	100	201	0	201

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_373 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_373 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000143	1 retrocopy	retro_amel_1291,
Canis familiaris	ENSCAFG00000018384	2 retrocopies	retro_cfam_1473, retro_cfam_1641,
Callithrix jacchus	ENSCJAG00000005125	1 retrocopy	retro_cjac_373 ,
Dasypus novemcinctus	ENSDNOG00000008384	1 retrocopy	retro_dnov_1894,
Echinops telfairi	ENSETEG00000004900	2 retrocopies	retro_etel_23, retro_etel_48,
Felis catus	ENSFCAG00000007057	2 retrocopies	retro_fcat_1035, retro_fcat_127,
Loxodonta africana	ENSLAFG00000029398	1 retrocopy	retro_lafr_844,
Microcebus murinus	ENSMICG00000002757	3 retrocopies	retro_mmur_322, retro_mmur_411, retro_mmur_974,
Myotis lucifugus	ENSMLUG00000015742	4 retrocopies	retro_mluc_139, retro_mluc_1580, retro_mluc_2564, retro_mluc_86,
Mus musculus	ENSMUSG00000016319	4 retrocopies	retro_mmus_1173, retro_mmus_1955, retro_mmus_2589, retro_mmus_459,
Oryctolagus cuniculus	ENSOCUG00000013268	11 retrocopies	retro_ocun_1002, retro_ocun_1233, retro_ocun_1457, retro_ocun_1694, retro_ocun_1705, retro_ocun_1862, retro_ocun_1877, retro_ocun_1890, retro_ocun_1932, retro_ocun_610, retro_ocun_708,
Otolemur garnettii	ENSOGAG00000010008	7 retrocopies	retro_ogar_1131, retro_ogar_1275, retro_ogar_1669, retro_ogar_2161, retro_ogar_2408, retro_ogar_2450, retro_ogar_2474,
Pteropus vampyrus	ENSPVAG00000014924	2 retrocopies	retro_pvam_1118, retro_pvam_911,
Rattus norvegicus	ENSRNOG00000039980	11 retrocopies	retro_rnor_1242, retro_rnor_1364, retro_rnor_1475, retro_rnor_1612, retro_rnor_1904, retro_rnor_1922, retro_rnor_2533, retro_rnor_2758, retro_rnor_721, retro_rnor_722, retro_rnor_723,
Ictidomys tridecemlineatus	ENSSTOG00000020438	3 retrocopies	retro_itri_314, retro_itri_532, retro_itri_868,
Tupaia belangeri	ENSTBEG00000006008	4 retrocopies	retro_tbel_1558, retro_tbel_1860, retro_tbel_4654, retro_tbel_4661,