RetrogeneDB ID: retro_cjac_225

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:5435307..5436120(-)
• Located in intron of: ENSCJAG00000007565

Retrocopy information

• Ensembl ID: ENSCJAG00000033849
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000009473
• Aliases: None
• Description: None

Sequence

>retro_cjac_225
ATGTGGAACAGTGGATTCGAAAGCTTTGGCAGCTCCAGCTACGGGGGAGCTGGCGGCTACACGCAGTCCCCGGGGGGCTT
TGGATCGCCCGGACCTTCTCAGGCCGAAAAGAAATCAAGAGCCCGAGCCCAGCACATTGTGCCCTGCACTATATCTCAGC
TGCTTTCTGCCACTTTGGTTGATGAAGTGTTCAGAATTGGGAATGTTGAGATTTCACAGGTCACTATTGTGGGGATCATC
AGACATACAGAGAAGGCCCCAACCAACATAGTTTACAAAATAGATGACATGACAGCTCCACCCATGGATGTTCGCCAGTG
GGTTGACACAGATGACGCCAGCAGTGAAAACACTGTGGTTCCTCCAGAAACATATTGGAAAGTGGCAGGCCACCTGAGAT
CTTTTCAGAACAAAAAGAGCCTGGTAGCCTTTAAGATCATGCCCCTGGAGGATATGAATGAGTTCACTGCACATATTCTA
GAAGTGATTAATGCACACATGATATTAAGCAAAGCCAGTGGTCAGCCCTCAGCAGGGAAAGCACCCATCAGCAATCCAGG
AATGAGTGAAGCAGGGAACTTTGGTGGGAATAGCTTTATGCCAGCAAATGGCCTCACTGTGGCCCAAAATCAGGTGCTGA
ATTTGATTAAGGCTTGTCCAAGACCTGAAGGGTTGAACTTTCAAGAGCTCAGGAACCAGCTGAAACACATGTCTGTACCC
TCAATCAAGCAAGCTGTGGATTTTCTGAGCAATGAGGGGCACATCTATTCTACTGTGGATGATGATCATTTTAAATCCAC
AGATGCAGAATAA

Alignment

ORF - retro_cjac_225 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.26 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MWNSGFESFGSSNYGGAGGYTQSPGGFGSPGPSQAEKKSRARAQHIVPCTISQLLSATLVDEVFRIGNVE
          MWNSGFESFGSS.YGGAGGYTQSPGGFGSPGPSQAEKKSRARAQHIVPCTISQLLSATLVDEVFRIGNVE
Retrocopy MWNSGFESFGSSSYGGAGGYTQSPGGFGSPGPSQAEKKSRARAQHIVPCTISQLLSATLVDEVFRIGNVE

Parental  ISQVTIVGIIRHTEKAPTNIVYKIDDMTAPPMDVRQWVDTDDASSENTVVPPETYVKVAGHLRSFQNKKS
          ISQVTIVGIIRHTEKAPTNIVYKIDDMTAPPMDVRQWVDTDDASSENTVVPPETY.KVAGHLRSFQNKKS
Retrocopy ISQVTIVGIIRHTEKAPTNIVYKIDDMTAPPMDVRQWVDTDDASSENTVVPPETYWKVAGHLRSFQNKKS

Parental  LVAFKIMPLEDMNEFTAHILEVINAHMILSKASGQPSAGKAPISNPGMSEAGNFGGNSFMPANGLTVAQN
          LVAFKIMPLEDMNEFTAHILEVINAHMILSKASGQPSAGKAPISNPGMSEAGNFGGNSFMPANGLTVAQN
Retrocopy LVAFKIMPLEDMNEFTAHILEVINAHMILSKASGQPSAGKAPISNPGMSEAGNFGGNSFMPANGLTVAQN

Parental  QVLNLIKACPRPEGLNFQELRNQLKHMSVPSIKQAVDFLSNEGHIYSTVDDDHFKSTDAE
          QVLNLIKACPRPEGLNFQELRNQLKHMSVPSIKQAVDFLSNEGHIYSTVDDDHFKSTDAE
Retrocopy QVLNLIKACPRPEGLNFQELRNQLKHMSVPSIKQAVDFLSNEGHIYSTVDDDHFKSTDAE

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	0.33 RPM	5.44 RPM
SRP051959_heart	0.32 RPM	5.98 RPM
SRP051959_kidney	0.47 RPM	5.32 RPM
SRP051959_liver	0.15 RPM	4.81 RPM
SRP051959_lung	0.41 RPM	11.19 RPM
SRP051959_lymph_node	0.41 RPM	17.58 RPM
SRP051959_skeletal_muscle	0.22 RPM	6.33 RPM
SRP051959_spleen	0.29 RPM	13.53 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_225 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_225 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_225 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006225	5 retrocopies	retro_btau_1093, retro_btau_1228, retro_btau_1359, retro_btau_406, retro_btau_633,
Callithrix jacchus	ENSCJAG00000009473	1 retrocopy	retro_cjac_225 ,
Homo sapiens	ENSG00000117748	2 retrocopies	retro_hsap_704, retro_hsap_815,
Gorilla gorilla	ENSGGOG00000015287	2 retrocopies	retro_ggor_599, retro_ggor_668,
Loxodonta africana	ENSLAFG00000014387	1 retrocopy	retro_lafr_519,
Macaca mulatta	ENSMMUG00000018172	2 retrocopies	retro_mmul_1081, retro_mmul_2172,
Nomascus leucogenys	ENSNLEG00000009702	3 retrocopies	retro_nleu_1409, retro_nleu_250, retro_nleu_2511,
Oryctolagus cuniculus	ENSOCUG00000016194	1 retrocopy	retro_ocun_1180,
Otolemur garnettii	ENSOGAG00000015583	2 retrocopies	retro_ogar_1838, retro_ogar_2066,
Pongo abelii	ENSPPYG00000001651	2 retrocopies	retro_pabe_523, retro_pabe_728,
Pan troglodytes	ENSPTRG00000000420	1 retrocopy	retro_ptro_566,
Pteropus vampyrus	ENSPVAG00000001449	1 retrocopy	retro_pvam_166,
Ictidomys tridecemlineatus	ENSSTOG00000004433	2 retrocopies	retro_itri_1257, retro_itri_773,
Tarsius syrichta	ENSTSYG00000010706	2 retrocopies	retro_tsyr_1184, retro_tsyr_1806,
Tursiops truncatus	ENSTTRG00000007507	1 retrocopy	retro_ttru_873,