RetrogeneDB ID: retro_cjac_56

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:150028397..150029282(+)
• Located in intron of: ENSCJAG00000018140

Retrocopy information

• Ensembl ID: ENSCJAG00000018138
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ACTB
• Ensembl ID: ENSCJAG00000000008
• Aliases: None
• Description: actin, beta [Source:HGNC Symbol;Acc:132]

Sequence

>retro_cjac_56
ATGGAGAAGATCTGGCACCACACTTTTTACAACGAGCTGCGTGTGGCTCCTGAGGAGCACCCCGTGCTGCTTACTGAGGC
CCCCCTGAACCCCAAGGCCAACCGTGAGAAGATGACCCAGATCATGTTTGAGACCTTCAACACCCCAGCCATGTATGTGG
CCATCCAGGCTGTGCTTTCCTTGTACGCCTCTGGCCGTACCACTGGCATCGTGATGGACTCCGGTGACGGGGTCACCCAC
ACTGTGCCCATCTATGAGGGGTATGCCGTCCCCCACGCCATCCTACATCTGGACCTGGCTGGCCGGGACCTGACTGACTA
CCTCATGAAGATCCTCACCGAGCGCGGCTACAGCTTCACCACCACAGCTGAGCGGGAAATCCTGCGTGACATCAAGGAGA
AGCTGTGCTACGTCGCCCTGGACTTCGAGCAGGAGATGGCCACGGCGGCCTCCAGCTCCTCCCTGGAGAAGAGCTATGAG
CTGCCCGATGGTCAGGTCATCACCATCGGCAACGAGCGGTTCCGCTGCCCTGAGGCACTCTTCCAGCCTTCTTTCCTGGG
CATGGAATCTTGTGGCATCCACGAAACTACCTTTAACTCCATCATGAAATGTGACGTGGACATCCGCAAAGACCTGTATG
CCAACACAGTGCTGTCTGGTGGTACCACCATGTACCCTGGCATCGCTGACAGGATGCAGAAGGAGATCACCGCCCCGGCA
CCCAGCACAATGAAGATCAAGATCATTGCTCCTCCCGAGCGCAAGTACTCAGTGTGGATTGGTGGCTCCATCCTGGCCTC
GCTGTCCACCTTCCAGCAGATGTGGATCAGCAAGCAGGAGTATGATGAGTCCGGCCCCTCCATCGTCCACCACAAATGCT
TCTAG

Alignment

ORF - retro_cjac_56 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGI
          MEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGI
Retrocopy MEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGI

Parental  VMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVAL
          VMDSGDGVTHTVPIYEGYA.PHAIL.LDLAGRDLTDYLMKILTERGYSFTTTAEREI.RDIKEKLCYVAL
Retrocopy VMDSGDGVTHTVPIYEGYAVPHAILHLDLAGRDLTDYLMKILTERGYSFTTTAEREILRDIKEKLCYVAL

Parental  DFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRK
          DFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRK
Retrocopy DFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRK

Parental  DLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQE
          DLYANTVLSGGTTMYPGIADRMQKEITA.APSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQE
Retrocopy DLYANTVLSGGTTMYPGIADRMQKEITAPAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQE

Parental  YDESGPSIVHRKCF
          YDESGPSIVH.KCF
Retrocopy YDESGPSIVHHKCF

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	40.47 RPM	474.83 RPM
SRP051959_heart	17.51 RPM	206.24 RPM
SRP051959_kidney	19.57 RPM	218.20 RPM
SRP051959_liver	7.32 RPM	80.30 RPM
SRP051959_lung	26.81 RPM	291.63 RPM
SRP051959_lymph_node	39.68 RPM	413.82 RPM
SRP051959_skeletal_muscle	7.12 RPM	85.32 RPM
SRP051959_spleen	34.62 RPM	347.02 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_56 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_56 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_56 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000010147	1 retrocopy	retro_apla_2,
Canis familiaris	ENSCAFG00000016020	3 retrocopies	retro_cfam_120, retro_cfam_260, retro_cfam_934,
Callithrix jacchus	ENSCJAG00000000008	2 retrocopies	retro_cjac_243, retro_cjac_56 ,
Callithrix jacchus	ENSCJAG00000002885	3 retrocopies	retro_cjac_139, retro_cjac_336, retro_cjac_377,
Dipodomys ordii	ENSDORG00000010079	1 retrocopy	retro_dord_11,
Equus caballus	ENSECAG00000015935	2 retrocopies	retro_ecab_271, retro_ecab_994,
Felis catus	ENSFCAG00000006788	1 retrocopy	retro_fcat_1613,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Macaca mulatta	ENSMMUG00000011153	1 retrocopy	retro_mmul_135,
Otolemur garnettii	ENSOGAG00000008348	1 retrocopy	retro_ogar_2637,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pan troglodytes	ENSPTRG00000018890	27 retrocopies	retro_ptro_1042, retro_ptro_1051, retro_ptro_1076, retro_ptro_1143, retro_ptro_1272, retro_ptro_1515, retro_ptro_1756, retro_ptro_178, retro_ptro_2122, retro_ptro_2173, retro_ptro_2349, retro_ptro_2454, retro_ptro_263, retro_ptro_2805, retro_ptro_2854, retro_ptro_314, retro_ptro_3207, retro_ptro_3219, retro_ptro_3282, retro_ptro_3287, retro_ptro_3292, retro_ptro_3302, retro_ptro_3307, retro_ptro_387, retro_ptro_432, retro_ptro_53, retro_ptro_584,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,