RetrogeneDB ID: retro_cjac_3276

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:20275462..20276230(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000001031
• Aliases: None
• Description: None

Sequence

>retro_cjac_3276
ATGGCCAGACCCGGCATGGAGCTGTGGCACGACCAGCTGGCGCTGGTGAAGGAAGCCTCAGTGGGCATTGGCGCGGCCGT
GGCCCAGGCCCTGGTCCAGCAGGGGCTGAAGGTGGTGGGCTGCGCCCACACCGTGGGCAACATCGAGGAGCTGGCTGCTG
AATGTTAAGAGTGCATGCTACCCCTGGACTTTGATCCCCTACAGATGTGACCTGTCAAATGAGGAGGACATCCTCTCCAT
GTTCTCGGCTATCCGTTCTCAGCACAGTGGCATAGACATCTGCATCAACAATACCGCTTGGGCCGGCCTGACTCCCTGCT
CTCAGGCAGCACCAGCGGTTGGAAGAAGATGCTCAATGTGAACACGCTGGCCCTCAGCATCTGCACGCGGGAAGCCTACC
AGTCCATGAAGGAGTGGAATGTGGACCATGGGCACATCATTAACATCAATAGCATGTCTGGCCACCGAGTGGTCCCCCAG
TCTGTGACCCACTTCTATAGTGCCACCAAGTATGCTGTCACTACACTGACGGAGGGACTGAGGCAAGAGCTTCGGGAGGC
CCAGACCCACAACTGAGCCACATGCATCTTTCCAGGTGTTGTGGAAACACAATTTGCCTTCAGACTCCACGACAAGGACC
CTGAGAAGGCAGCTGCCACCTATGAGCACATGAAATGTCTCCAACCTGAGGATGTGGCCGAGGCTGTTATCTACGTCCTC
AGCACCCCCGCAAACGTCCAGATTGGAGACATCGAGATGAGGCCCACG

Alignment

ORF - retro_cjac_3276 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.85 %
• Parental protein coverage: 98.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MARRGMERWRDRLALVTGASVGIGAAVARALVQQGLKVVGCARTVGNIEELAAEC-KSAGYPGTLIPYRC
          MAR.GME.W.D.LALV..ASVGIGAAVA.ALVQQGLKVVGCA.TVGNIEELAAEC.KSA.YP.TLIPYRC
Retrocopy MARPGMELWHDQLALVKEASVGIGAAVAQALVQQGLKVVGCAHTVGNIEELAAEC>KSACYPWTLIPYRC

Parental  DLSNEEDILSMFSAIRSQHSGVDICINNAG-LGRPDSLLSGSTSGWKEMLNVNVLALSICTREAYQSMKE
          DLSNEEDILSMFSAIRSQHSG.DICINN...LGRPDSLLSGSTSGWK.MLNVN.LALSICTREAYQSMKE
Retrocopy DLSNEEDILSMFSAIRSQHSGIDICINNTA<LGRPDSLLSGSTSGWKKMLNVNTLALSICTREAYQSMKE

Parental  RNVDDGHIININSMSGHRVVPQSVTHFYSATKYAVTALTEGLRQELREAQTHIRATAQCISPGVVETQFA
          .NVD.GHIININSMSGHRVVPQSVTHFYSATKYAVT.LTEGLRQELREAQTH..AT..CI.PGVVETQFA
Retrocopy WNVDHGHIININSMSGHRVVPQSVTHFYSATKYAVTTLTEGLRQELREAQTHN*AT--CIFPGVVETQFA

Parental  FRLHDKDPEKAAATYEHMKCLQPEDVTEAVIYVLSTPPHVQIGDIQMRPT
          FRLHDKDPEKAAATYEHMKCLQPEDV.EAVIYVLSTP..VQIGDI.MRPT
Retrocopy FRLHDKDPEKAAATYEHMKCLQPEDVAEAVIYVLSTPANVQIGDIEMRPT

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	17.75 RPM
SRP051959_heart	0.00 RPM	11.47 RPM
SRP051959_kidney	0.02 RPM	13.36 RPM
SRP051959_liver	0.00 RPM	12.26 RPM
SRP051959_lung	0.00 RPM	9.30 RPM
SRP051959_lymph_node	0.00 RPM	16.12 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.80 RPM
SRP051959_spleen	0.00 RPM	11.79 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3276 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3276 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3276 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001031	2 retrocopies	retro_cjac_3276 , retro_cjac_3277,
Oryctolagus cuniculus	ENSOCUG00000021228	1 retrocopy	retro_ocun_1204,