RetrogeneDB ID: retro_cjac_1033

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:44379611..44380454(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC61
• Ensembl ID: ENSCJAG00000012104
• Aliases: None
• Description: coiled-coil domain containing 61 [Source:HGNC Symbol;Acc:33629]

Sequence

>retro_cjac_1033
ATGGGCCAGCTGGCCGGCCTGCAGGTGGACTACGTTTTCCGGGGTGTGGAGCATGCTGTGCAGGTGGTGGTTACCGGGCA
GGTGCTGGAGCTGAAGGTGGAGGACCGGATGACTGTGGTCCAGTGGGGGGGCGAGTTCGATGCCGGCTTCATTGAAAATT
TGACTCACAAGACAGGGAACTTCAAACAGTTCAACATCTTCTGTCATATGCTGGAGTCAGCCCTCACTCAGAGCAGTGAG
TCAGTCACTCTGGACCTGCTTACCTACACAGACCTGGAGTCCCTGCGGAACCACAAGTTGGGGGGCCGTCCAGGCCCTCT
GGCCCCCAGATCGGCCTAGTTCAACTCCAAGCGCTACCTAATCCTCATCTACTCAGTGGAGTTTGACAGGATTCACTACC
CGCTGCCCCTCCCGTACCAGGGCAAGCCAGACCCTGTGGTTCTGCAGGGCATCATCCACTCACTGAAGGAGGAACTGAGC
CGCCTGCAAGGGCTGGGCGGCCAGGATACTCGGGACACCCGGGAGACTGAGATCTGGCACCTGCGGGAGCAGGTGACGCG
CCTGGCATCAGAGAAGCGCGAGCTGGAGGTGCAGCCGGGCCGATCGCGCGAGGAAGCGCTGGCTGGGCGCGCGGCCCGCC
AGGAGGCCAAGGCATTGCGTGGGTTGGTGCGTGGGCTGGAGCTGGAGCTACTGCAGGAGCGCGTCCTTGGGCATAGGGTG
GCTGGCCGCCGAGGCTAGGACTGCCGCCGCCTGGCCAAGGAGCTCGAGGAGGCGAAGGCATCCGAGCGGAGCCTGCAAGC
CCAGCTGAAGACGCTGACCAGCGAGCTGGCCTTGTACAAGAGG

Alignment

ORF - retro_cjac_1033 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.81 %
• Parental protein coverage: 58.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDQPAGLQVDYVFRGVEHAVRVVVSGQVLELEVEDRMTADQWRGEFDAGFIEDLTHKTGNFKQFNIFCHM
          M.Q.AGLQVDYVFRGVEHAV.VVV.GQVLEL.VEDRMT..QW.GEFDAGFIE.LTHKTGNFKQFNIFCHM
Retrocopy MGQLAGLQVDYVFRGVEHAVQVVVTGQVLELKVEDRMTVVQWGGEFDAGFIENLTHKTGNFKQFNIFCHM

Parental  LESALTQSSESVTLDLLTYTDLESLRNRKMGGRPGPLAPRSAQLNSKRYLILIYSVEFDRIHYPLPLPYQ
          LESALTQSSESVTLDLLTYTDLESLRN.K.GGRPGPLAPRSA..NSKRYLILIYSVEFDRIHYPLPLPYQ
Retrocopy LESALTQSSESVTLDLLTYTDLESLRNHKLGGRPGPLAPRSA*FNSKRYLILIYSVEFDRIHYPLPLPYQ

Parental  GKPDPVVLQGIIRSLKEELGRLQGLGGQDTRDTRETEIWHLREQVSRLASEKRELEVQLGRSREEALAGR
          GKPDPVVLQGII.SLKEEL.RLQGLGGQDTRDTRETEIWHLREQV.RLASEKRELEVQ.GRSREEALAGR
Retrocopy GKPDPVVLQGIIHSLKEELSRLQGLGGQDTRDTRETEIWHLREQVTRLASEKRELEVQPGRSREEALAGR

Parental  AARQEAEALRGLVRGLELELRQERGLGHRVAGRRGQDCRRLAKELEEAKASERSLRARLKTLTSELALYK
          AARQEA.ALRGLVRGLELEL.QER.LGHRVAGRRG.DCRRLAKELEEAKASERSL.A.LKTLTSELALYK
Retrocopy AARQEAKALRGLVRGLELELLQERVLGHRVAGRRG*DCRRLAKELEEAKASERSLQAQLKTLTSELALYK

Parental  R
          R
Retrocopy R

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	0.00 RPM	1.29 RPM
SRP051959_heart	0.00 RPM	2.32 RPM
SRP051959_kidney	0.00 RPM	1.66 RPM
SRP051959_liver	0.00 RPM	1.19 RPM
SRP051959_lung	0.03 RPM	2.90 RPM
SRP051959_lymph_node	0.00 RPM	2.60 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.57 RPM
SRP051959_spleen	0.00 RPM	1.81 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1033 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1033 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1033 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012104	1 retrocopy	retro_cjac_1033 ,