RetrogeneDB ID: retro_cjac_353

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:60834323..60834635(-)
• Located in intron of: ENSCJAG00000015325

Retrocopy information

• Ensembl ID: ENSCJAG00000023131
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000004864
• Aliases: None
• Description: None

Sequence

>retro_cjac_353
AAAATGGACGTTCCTAAAACCCGCCGGACTTTCCGTAAGAAGTGTGGCAAGCACCAACCCCACAAAGTGACACAGTACAA
GATGGGCAAGGATTCTCTGTACGCCCAGGGAAAGCGGCGTTATGACAGGGAGCAGAGTGGCTATGGTGGGCAAACTAAGC
CGATTTTCCAGAAAAAGGCTAAGACTACAAAGAAGATTGTGCTATGCGTTGAGCCCAACTGCAGATCTAAGAGAATGCTG
GCTATTAAAAGATGCAAACATTTTGAACTGGGAGGAGATAAGAAGAGAAGGGGCCAAGTGATCCAGTTCTAA

Alignment

ORF - retro_cjac_353 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.48 %
• Parental protein coverage: 99.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRLE
          ..VPKTRRTF.KKCGKHQPHKVTQYK.GKDSLYAQGKRRYDR.QSGYGGQTKPIF.KKAKTTKKIVL...
Retrocopy MDVPKTRRTFRKKCGKHQPHKVTQYKMGKDSLYAQGKRRYDREQSGYGGQTKPIFQKKAKTTKKIVL---

Parental  CVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF
          CVEPNCRSKRMLAIKRCKHFELGGDKKR.GQVIQF
Retrocopy CVEPNCRSKRMLAIKRCKHFELGGDKKRRGQVIQF

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	24.01 RPM
SRP051959_heart	0.02 RPM	24.96 RPM
SRP051959_kidney	0.20 RPM	36.05 RPM
SRP051959_liver	0.04 RPM	31.34 RPM
SRP051959_lung	0.08 RPM	39.99 RPM
SRP051959_lymph_node	0.11 RPM	70.39 RPM
SRP051959_skeletal_muscle	0.02 RPM	25.62 RPM
SRP051959_spleen	0.06 RPM	56.81 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_353 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_353 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_353 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 126 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008503	1 retrocopy	retro_acar_98,
Ailuropoda melanoleuca	ENSAMEG00000009384	1 retrocopy	retro_amel_85,
Callithrix jacchus	ENSCJAG00000004864	4 retrocopies	retro_cjac_304, retro_cjac_353 , retro_cjac_55, retro_cjac_72,
Equus caballus	ENSECAG00000015464	9 retrocopies	retro_ecab_129, retro_ecab_131, retro_ecab_204, retro_ecab_219, retro_ecab_265, retro_ecab_268, retro_ecab_294, retro_ecab_543, retro_ecab_646,
Homo sapiens	ENSG00000241343	14 retrocopies	retro_hsap_1477, retro_hsap_1508, retro_hsap_1595, retro_hsap_1782, retro_hsap_2, retro_hsap_2015, retro_hsap_2274, retro_hsap_2632, retro_hsap_3461, retro_hsap_3819, retro_hsap_3981, retro_hsap_4154, retro_hsap_4299, retro_hsap_647,
Homo sapiens	ENSG00000257529	1 retrocopy	retro_hsap_1353,
Monodelphis domestica	ENSMODG00000025578	2 retrocopies	retro_mdom_1878, retro_mdom_971,
Mus musculus	ENSMUSG00000079435	1 retrocopy	retro_mmus_4,
Nomascus leucogenys	ENSNLEG00000007540	27 retrocopies	retro_nleu_1003, retro_nleu_1243, retro_nleu_1291, retro_nleu_153, retro_nleu_157, retro_nleu_1632, retro_nleu_178, retro_nleu_1833, retro_nleu_1903, retro_nleu_1959, retro_nleu_2145, retro_nleu_2345, retro_nleu_2381, retro_nleu_2699, retro_nleu_2965, retro_nleu_2995, retro_nleu_2996, retro_nleu_3027, retro_nleu_3028, retro_nleu_3059, retro_nleu_3111, retro_nleu_385, retro_nleu_453, retro_nleu_644, retro_nleu_805, retro_nleu_842, retro_nleu_991,
Otolemur garnettii	ENSOGAG00000004551	6 retrocopies	retro_ogar_1160, retro_ogar_1681, retro_ogar_2390, retro_ogar_2519, retro_ogar_294, retro_ogar_470,
Pongo abelii	ENSPPYG00000025837	37 retrocopies	retro_pabe_1141, retro_pabe_1174, retro_pabe_121, retro_pabe_1226, retro_pabe_1256, retro_pabe_1311, retro_pabe_141, retro_pabe_1463, retro_pabe_1539, retro_pabe_154, retro_pabe_1540, retro_pabe_1616, retro_pabe_1650, retro_pabe_1651, retro_pabe_1944, retro_pabe_195, retro_pabe_2011, retro_pabe_2331, retro_pabe_2443, retro_pabe_2622, retro_pabe_2857, retro_pabe_296, retro_pabe_3057, retro_pabe_3151, retro_pabe_3273, retro_pabe_3372, retro_pabe_3687, retro_pabe_3704, retro_pabe_441, retro_pabe_449, retro_pabe_55, retro_pabe_573, retro_pabe_574, retro_pabe_667, retro_pabe_73, retro_pabe_772, retro_pabe_931,
Pteropus vampyrus	ENSPVAG00000001569	1 retrocopy	retro_pvam_17,
Rattus norvegicus	ENSRNOG00000011494	1 retrocopy	retro_rnor_259,
Sarcophilus harrisii	ENSSHAG00000013479	1 retrocopy	retro_shar_467,
Ictidomys tridecemlineatus	ENSSTOG00000027251	20 retrocopies	retro_itri_1171, retro_itri_1189, retro_itri_1364, retro_itri_1405, retro_itri_1471, retro_itri_161, retro_itri_1681, retro_itri_290, retro_itri_385, retro_itri_430, retro_itri_555, retro_itri_609, retro_itri_644, retro_itri_730, retro_itri_753, retro_itri_784, retro_itri_803, retro_itri_845, retro_itri_865, retro_itri_903,