RetrogeneDB ID: retro_cjac_681

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:43183276..43184085(+)
• Located in intron of: ENSCJAG00000021101

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNN1
• Ensembl ID: ENSCJAG00000005530
• Aliases: None
• Description: calponin 1, basic, smooth muscle [Source:HGNC Symbol;Acc:2155]

Sequence

>retro_cjac_681
ATGAGCTCCAGGCAGTTCAACAAGGGCCCCTCGTACGGGCTGTCGGCCAAGGTCAAGAACCGGCTCCTGTCCAAGTATGA
CCCTCAGAAGGAGGCAGAGCTCCGAAGCTGGATCGAGGGACTCACCGGTCTCTCCATCGGCCCCAAATTCCAGAAGGGCC
TGAAGGACGGGATTATCTTATGCACACTCATGAACAAGCTACAGCCAGGCTCAGTCCCCAAGATCAACCGCTCCATGCAG
AACTGGCACCAGCTAGAAAATCTTTCCAACTTCATCAAGGCCATGGTCAGCTACGGCATGAACCCCGTGGACCTGTTGGA
GGCCAACAACCTGTTTGAGAGCCGGAACATGACGCAGGTGCAGATGTCTCTTCTCGCCCTGGCGAAAAAGGCCAAGACTA
AGGGGCTGCAGAGTGGAATGGACATCGGCGTCAAGTACTTGGAGAAGCAGGAGTGGAACTTCGACGACGCCGCCAGTGCG
TCATCGGGCTGCAGATGGGCACCAACAAATGTGCCAGCCAGTCGGGCATGACCACGTACAGCACAAGGAGGCATCTCTAC
GACCCCAAGAACCACATCCTGCCCCTCATGGACCACTCAACCATCAGCCTCCAGATGGGCACCAACAAGTGTGCCAGCCA
GGTGGGCATGACGGCTCCCGGGACGCGGCGGCCTATCTATGACACCAAACTGGGAACCGACAAGTGTGATAACTCCTCCA
TGTCCCTGCAGATGGGCTACACCCAGGGCGCCAACCAGAGCGGCCTGGTCTTCGGCCTGGGCCGGCAGATATACGACCCC
AAGTACTGC

Alignment

ORF - retro_cjac_681 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.95 %
• Parental protein coverage: 91.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSAHFNRGPAYGLSAEVKNKLAQKYDHQREQELREWIEGVTGRRIGNNFMDGLKDGIILCEFINKLQPG
          MSS..FN.GP.YGLSA.VKN.L..KYD.Q.E.ELR.WIEG.TG..IG..F..GLKDGIILC...NKLQPG
Retrocopy MSSRQFNKGPSYGLSAKVKNRLLSKYDPQKEAELRSWIEGLTGLSIGPKFQKGLKDGIILCTLMNKLQPG

Parental  SVKKINESTQNWHQLENIGNFIKAITKYGVKPHDIFEANDLFENTNHTQVQSTLLALASMAKTKGNKVNV
          SV.KIN.S.QNWHQLEN..NFIKA...YG..P.D..EAN.LFE..N.TQVQ..LLALA...K.K......
Retrocopy SVPKINRSMQNWHQLENLSNFIKAMVSYGMNPVDLLEANNLFESRNMTQVQMSLLALAK--KAKTKGLQS

Parental  GVKYAEKQERKFE-PEKLREGRNIIGLQMGTNKFASQQGMTAYGTRRHLYDPKLGTDQPLDQATISLQMG
          G.....K...K.E..E..R.....IGLQMGTNK.ASQ.GMT.Y.TRRHLYDPK.......D..TISLQMG
Retrocopy GMDIGVKYLEKQE<VELRRRRQCVIGLQMGTNKCASQSGMTTYSTRRHLYDPKNHILPLMDHSTISLQMG

Parental  TNKGASQAGMTAPGTKRQIFEPGLGMEHCDTLNVSLQMGSNKGASQRGMTVYGLPRQVYDPKYC
          TNK.ASQ.GMTAPGT.R.I....LG...CD....SLQMG...GA.Q.G..V.GL.RQ.YDPKYC
Retrocopy TNKCASQVGMTAPGTRRPIYDTKLGTDKCDNSSMSLQMGYTQGANQSGL-VFGLGRQIYDPKYC

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	0.67 RPM	66.45 RPM
SRP051959_heart	0.51 RPM	67.49 RPM
SRP051959_kidney	0.49 RPM	2.15 RPM
SRP051959_liver	0.58 RPM	0.11 RPM
SRP051959_lung	0.81 RPM	6.85 RPM
SRP051959_lymph_node	0.91 RPM	0.84 RPM
SRP051959_skeletal_muscle	0.33 RPM	2.75 RPM
SRP051959_spleen	0.42 RPM	1.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_681 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_681 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_681 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000062	1 retrocopy	retro_amel_675,
Callithrix jacchus	ENSCJAG00000005530	1 retrocopy	retro_cjac_681 ,
Callithrix jacchus	ENSCJAG00000006156	2 retrocopies	retro_cjac_2035, retro_cjac_2444,
Callithrix jacchus	ENSCJAG00000012755	2 retrocopies	retro_cjac_723, retro_cjac_778,
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Tursiops truncatus	ENSTTRG00000001803	1 retrocopy	retro_ttru_1792,