RetrogeneDB ID: retro_cjac_1727

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:8395646..8396666(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNB2
• Ensembl ID: ENSCJAG00000015074
• Aliases: None
• Description: None

Sequence

>retro_cjac_1727
ATGAGTGAGCTGGAGCAATTGAGACAGGAGGCCGAGCAGCTCCGGAACCAGATCGGGGATGCCCGAAAAGCATGTGGGGA
CTCAACACTGACCCAGATCACAGCTGGGCTGGACCCAGTGGGGAGAATCCAGATGAAGACCCGGAGGGCCCTCCGTGGGC
ATCTGGCAAAGATCTATGCCATGCACTGGGGGACCGACTCAAGGCTGCTGGTAAGCGCCTCCCAGGATGGGAAGCTCATC
ATCTGGGACAGCTACACCACCAACAAAGTCTATGCCATCCAGCTACGCTCCTCCTAAGTCATGACCTGTGCCTACGCGCC
CTCAGGGAACTTTGTGGCCTGTGGGGGTTTGGACAACATCTGCTTCATCTACAACCTCAAGACCCGAGAGGGCAACGTCG
GGGTCAGCCGGGAGCTGCCTGGCCACACTGGGTACCTGTCGTGCTGCCGCTTCCTGGATGACAAGCAAATCATCACCAGC
CCTGGGGATACCACCTGTGCCCTGTGGGACATTGAGACAGGCCAGCAGACAGTGGGTTTTGCTGGACACAGTGGGGATGT
GATGTCCCTGGCCCTGGCCCCTGATGGCCGCACGTTTGTGTCAGGAGCCTGTGACGCCTCTATCAAGCTGTGGGACGTTC
AGGATTCCATGTGCCGACAGACCTTTATCGGCCACGAATCTGACATCAACGCCGTGGCTTTCTTCCCCAACCGCTATGCC
TTTACCACTGGCTCTGATGATGCCACGTGCCGCCTCTTCGACCTGAGGGCCGATCAGGGGCTCCTCAGGTACTCCCACGA
CAACATCATCTGTGGCATCACCTCTGTTGCCTTCTCTCACAGCGGCTGGCTGCTGCTTGCTGGCTATGACGATTTCAACT
GCAACATCTGGGATGCCATGAAGGGCGACCGTGCAGGGGTCCTCGCTGGCCGCCACAACCGCGTGAGCTGCCTCGGGGTC
ACTGATGATGGCATGGCTGTGGCCACGGGCTCCTGGGACTCCTTCCTCAAGATCTGGAAC

Alignment

ORF - retro_cjac_1727 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSELEQLRQEAEQLRNQIRDARKACGDSTLTQITAGLDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLL
          MSELEQLRQEAEQLRNQI.DARKACGDSTLTQITAGLDPVGRIQM.TRR.LRGHLAKIYAMHWGTDSRLL
Retrocopy MSELEQLRQEAEQLRNQIGDARKACGDSTLTQITAGLDPVGRIQMKTRRALRGHLAKIYAMHWGTDSRLL

Parental  VSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNFVACGGLDNICSIYSLKTREGNVRVSRELP
          VSASQDGKLIIWDSYTTNKV.AI.LRSS.VMTCAYAPSGNFVACGGLDNIC.IY.LKTREGNV.VSRELP
Retrocopy VSASQDGKLIIWDSYTTNKVYAIQLRSS*VMTCAYAPSGNFVACGGLDNICFIYNLKTREGNVGVSRELP

Parental  GHTGYLSCCRFLDDNQIITSSGDTTCALWDIETGQQTVGFAGHSGDVMSLSLAPDGRTFVSGACDASIKL
          GHTGYLSCCRFLDD.QIITS.GDTTCALWDIETGQQTVGFAGHSGDVMSL.LAPDGRTFVSGACDASIKL
Retrocopy GHTGYLSCCRFLDDKQIITSPGDTTCALWDIETGQQTVGFAGHSGDVMSLALAPDGRTFVSGACDASIKL

Parental  WDVRDSMCRQTFIGHESDINAVAFFPNGYAFTTGSDDATCRLFDLRADQELLMYSHDNIICGITSVAFSR
          WDV.DSMCRQTFIGHESDINAVAFFPN.YAFTTGSDDATCRLFDLRADQ.LL.YSHDNIICGITSVAFS.
Retrocopy WDVQDSMCRQTFIGHESDINAVAFFPNRYAFTTGSDDATCRLFDLRADQGLLRYSHDNIICGITSVAFSH

Parental  SGRLLLAGYDDFNCNIWDAMKGDRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN
          SG.LLLAGYDDFNCNIWDAMKGDRAGVLAG..NRVSCLGVTDDGMAVATGSWDSFLKIWN
Retrocopy SGWLLLAGYDDFNCNIWDAMKGDRAGVLAGRHNRVSCLGVTDDGMAVATGSWDSFLKIWN

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	16.73 RPM
SRP051959_heart	0.00 RPM	10.72 RPM
SRP051959_kidney	0.00 RPM	13.49 RPM
SRP051959_liver	0.00 RPM	7.28 RPM
SRP051959_lung	0.00 RPM	12.20 RPM
SRP051959_lymph_node	0.00 RPM	11.55 RPM
SRP051959_skeletal_muscle	0.02 RPM	8.15 RPM
SRP051959_spleen	0.00 RPM	10.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1727 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1727 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1727 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015074	1 retrocopy	retro_cjac_1727 ,
Macropus eugenii	ENSMEUG00000003863	1 retrocopy	retro_meug_1275,
Monodelphis domestica	ENSMODG00000004610	1 retrocopy	retro_mdom_880,