RetrogeneDB ID: retro_cjac_738

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:116559160..116559961(+)
• Located in intron of: ENSCJAG00000017801

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000020803
• Aliases: None
• Description: None

Sequence

>retro_cjac_738
ATGGCAGTGACCAAGAAGCTCTTACAGATGGACCTGTAAGGGCTGCTAGGAATTGAGGAGAAGGTGGCGGACAAAGAGGT
GAAGAAGGCATATAGACAGTAGGCCCTCCCCTGCCACACAGACAAAAATCCAGATAATCCCAGAGCAGCTGAACTCCTCC
ACCTGCTTTCTCAGGCCTTGGAGGCACTGACTGATGCTGCAGCCAGAGCTGTGTATGACAAGATCAGGAAAGCCAAGAAG
CAGGCAGCAGAGACGACCCAGAAACCTGATGAGGAAAGAAGTAAGGTGAAGCTTGATCTGGAGGCCCAGGAATGGCAGGC
CCAGGCCCAGGAAAGAGAGGAGGAGGAAAGTCGGGGCACCAGGACACTAGAGCAAGAGAACGAACCCCTGAGAAAAGAGG
GTTCCTGGCAGCTGGAGGAACAGCAGAGGCTGATCCGGGAGCAGATACAGGAGCATGACCAGAGATTGAGAGGAAAGACA
GAAAATACTGAAGGCCGAGGAACCCTCAAACTAAAACTAAAATGGAAGTGCAGGAAGGAGAATGAGTTAAAAGGTGGCTC
CAAAGACATCCTTCTACGACTTTTGCAAAAGTATGGTGCGGTTCTCAACCTGATGCTTTTTAGTAAGAAGGCAGGCACTG
CTGTGGTAGAGTTCGCGACCGTCAAGGCTGCGGAGCTGGCTGTCCAGAATGAAGTTGGCCTGGTGGATAACCCTCTGAAG
ATTTCCTGGTTGGAGGGACAGCCCCAGAGCACCGTGGGCCACCCAGCACCGTCAAAGGGCTCAGTGCTGTCACAGAGGGA
C

Alignment

ORF - retro_cjac_738 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.99 %
• Parental protein coverage: 89.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVTKELLQMDLYALLGIEEKAADKEVKKAFRQKALSCHPDKNPDNPRAAELFHQLSQALEVLTDAAARA
          MAVTK.LLQMDL..LLGIEEK.ADKEVKKA.RQ.AL.CH.DKNPDNPRAAEL.H.LSQALE.LTDAAARA
Retrocopy MAVTKKLLQMDL*GLLGIEEKVADKEVKKAYRQ*ALPCHTDKNPDNPRAAELLHLLSQALEALTDAAARA

Parental  AYDKVRKAKKQAAERTQKLDEKRKKVKLDLEARERQAQAQESEEEEESRSTRTLEQEIERLREEGSRQLE
          .YDK.RKAKKQAAE.TQK.DE.R.KVKLDLEA.E.QAQAQE..EEEESR.TRTLEQE.E.LR.EGS.QLE
Retrocopy VYDKIRKAKKQAAETTQKPDEERSKVKLDLEAQEWQAQAQE-REEEESRGTRTLEQENEPLRKEGSWQLE

Parental  EQQRLIREQIRQDHDQRLRGKTENTEGQGTPKLKLKWKCKKEDESKGGYSKDVLLQLLQKYGEVLNLVLS
          EQQRLIREQI.Q.HDQRLRGKTENTEG.GT.KLKLKWKC.KE.E.KGG.SKD.LL.LLQKYG.VLNL.L.
Retrocopy EQQRLIREQI-QEHDQRLRGKTENTEGRGTLKLKLKWKCRKENELKGG-SKDILLRLLQKYGAVLNLMLF

Parental  SKKAGTAVVEFATVRAAELAVQNEVGLVDNPLKISWLEGQPQDAMGRSHPGLSKGSVVSERD
          SKKAGTAVVEFATV.AAELAVQNEVGLVDNPLKISWLEGQPQ...G..HP..SKGSV.S.RD
Retrocopy SKKAGTAVVEFATVKAAELAVQNEVGLVDNPLKISWLEGQPQSTVG--HPAPSKGSVLSQRD

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	0.18 RPM	3.02 RPM
SRP051959_heart	0.11 RPM	3.47 RPM
SRP051959_kidney	0.20 RPM	5.15 RPM
SRP051959_liver	0.02 RPM	2.53 RPM
SRP051959_lung	0.24 RPM	5.84 RPM
SRP051959_lymph_node	0.48 RPM	5.91 RPM
SRP051959_skeletal_muscle	0.07 RPM	3.06 RPM
SRP051959_spleen	0.34 RPM	5.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_738 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_738 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_738 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020803	4 retrocopies	retro_cjac_1013, retro_cjac_4017, retro_cjac_738 , retro_cjac_820,
Cavia porcellus	ENSCPOG00000014110	1 retrocopy	retro_cpor_693,
Homo sapiens	ENSG00000104129	2 retrocopies	retro_hsap_2363, retro_hsap_3468,
Gorilla gorilla	ENSGGOG00000000051	1 retrocopy	retro_ggor_2340,
Macropus eugenii	ENSMEUG00000005641	2 retrocopies	retro_meug_1387, retro_meug_2001,
Myotis lucifugus	ENSMLUG00000014835	1 retrocopy	retro_mluc_317,
Macaca mulatta	ENSMMUG00000013160	1 retrocopy	retro_mmul_1574,
Mus musculus	ENSMUSG00000034278	1 retrocopy	retro_mmus_3346,
Nomascus leucogenys	ENSNLEG00000003257	1 retrocopy	retro_nleu_343,
Pongo abelii	ENSPPYG00000006360	1 retrocopy	retro_pabe_2864,
Pan troglodytes	ENSPTRG00000006929	2 retrocopies	retro_ptro_1729, retro_ptro_2351,
Rattus norvegicus	ENSRNOG00000012368	2 retrocopies	retro_rnor_18, retro_rnor_2319,