RetrogeneDB ID: retro_cjac_1041

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:56247147..56248101(-)
• Located in intron of: ENSCJAG00000019252

Retrocopy information

• Ensembl ID: ENSCJAG00000035474
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000021322
• Aliases: None
• Description: None

Sequence

>retro_cjac_1041
CACGGACACAGCCAGCAGCTGCAGCTGACTTGGAATGACCTGGGAGACAAATACAACAGCATGGAAGATGCCAAAGTCTA
CATGGCTAAAGTGGACTGCACGGCCAACTCTGACGTGTGCTCCACCCAGCGGGTGCGAGGATACCCTACGTAAAGTTTTT
CAAGCCAGGCCAAGAAGCTGTGAAGTACCAGGGTCCTCAGGACTTCCAGACATTGGAAAACTGGATGCTACAGACGCTGT
ATGAGAAGCAAGTGACACCAGAGCCAGAAGTGGAACCACCCAGAGCCCCTGAGCTGGGGCTGTATGAGCTCTCAGTGAGC
AACTTTGAGCTGCACATTGCACAAGGCAACCACTTTTATCAAGTTCTTGGCTCCATGGTGTGGTCACTGCAAAGCTCTGG
CTCCAACCTGGGAGCAGCTTGCTCTGGGCCTTGAACATTCTGAAACTGTCAAGATTGGCAAGGTTGATTGTACACAGCAC
TATGAACTCTGCTCCAGAAACCAGGTTCATGGCTATCCCACTCTTCTCTGGTTCCGAGATGGGAAAAAGGTTGCTCAGCA
TAAGGGAAAGCGCGATTTGGAGTCACTGAGGGATTACGTGGAGTCACAGCTGCAGTGCACAGAGACTGGAGCCGCAGAGA
CCATCACACCCTCAGAGGCCCTGGTGCTGGCAGCCGAGCCTGAAGATGACAAGGGCACTGTGTTGGCACTCACTGAGAAG
AATTTCGATGACACCATTGCAGAAGGAATAACCTTCATCAAGTTTTATGCTCCATGGTGTGGTCATTGTAAGAATCTGGC
TCCCACTTGGAAGGAACTCTCCAAAAAGGAATTCCCTGGTCTGGCAGGGGTCAAGATAGCCGAAGTAGACTGCACCACTG
AACAGAATATTTACAGCAAGTATTTGGTTCGAGGCTACCCTACATTGTTGCTTTTCTGAGGAGGGAAGAAAGTC

Alignment

ORF - retro_cjac_1041 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.51 %
• Parental protein coverage: 76.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YGHCQRLQPTWNDLGDKYNSMEDAKVYVAKVDCTADSDVCSAQGVRGYPT-LKFFKPGQEAVKYQGPRDF
          .GH.Q.LQ.TWNDLGDKYNSMEDAKVY.AKVDCTA.SDVCS.Q.VRGYPT..KFFKPGQEAVKYQGP.DF
Retrocopy HGHSQQLQLTWNDLGDKYNSMEDAKVYMAKVDCTANSDVCSTQRVRGYPT<VKFFKPGQEAVKYQGPQDF

Parental  QTLENWMLQTLNEEPVTPEPKVEPPRAPELKQGLYELSASNFELHIAQGDHF-IKFFAPWCGHCKALAPT
          QTLENWMLQTL.E..VTPEP.VEPPRAPEL..GLYELS.SNFELHIAQG.HF.IKF.APWCGHCKALAPT
Retrocopy QTLENWMLQTLYEKQVTPEPEVEPPRAPEL--GLYELSVSNFELHIAQGNHF>IKFLAPWCGHCKALAPT

Parental  WEQLALGLEHSETVKIGKVDCTQHYELCSGNQVRGYPTLLWFRDGEKVDQYKGKRDLESLREYVESQLQR
          WEQLALGLEHSETVKIGKVDCTQHYELCS.NQV.GYPTLLWFRDG.KV.Q.KGKRDLESLR.YVESQLQ.
Retrocopy WEQLALGLEHSETVKIGKVDCTQHYELCSRNQVHGYPTLLWFRDGKKVAQHKGKRDLESLRDYVESQLQC

Parental  TETGAAETVTPSEAPVLAAEPEADKGTVLALTEKNFDDTIAEGITFIKFYAPWCGHCKNLAPTWEELSKK
          TETGAAET.TPSEA.VLAAEPE.DKGTVLALTEKNFDDTIAEGITFIKFYAPWCGHCKNLAPTW.ELSKK
Retrocopy TETGAAETITPSEALVLAAEPEDDKGTVLALTEKNFDDTIAEGITFIKFYAPWCGHCKNLAPTWKELSKK

Parental  EFPGLAGVKIAEVDCTAERNICSKYSVRGYPTLLLFRGGKKV
          EFPGLAGVKIAEVDCT.E.NI.SKY.VRGYPTLLLF.GGKKV
Retrocopy EFPGLAGVKIAEVDCTTEQNIYSKYLVRGYPTLLLF*GGKKV

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	1.31 RPM	70.80 RPM
SRP051959_heart	0.91 RPM	33.55 RPM
SRP051959_kidney	0.84 RPM	46.06 RPM
SRP051959_liver	1.54 RPM	196.20 RPM
SRP051959_lung	1.42 RPM	34.58 RPM
SRP051959_lymph_node	2.10 RPM	44.95 RPM
SRP051959_skeletal_muscle	0.74 RPM	20.72 RPM
SRP051959_spleen	1.26 RPM	58.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1041 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1041 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1041 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002184	4 retrocopies	retro_chof_1163, retro_chof_2176, retro_chof_2312, retro_chof_663,
Callithrix jacchus	ENSCJAG00000021322	2 retrocopies	retro_cjac_1041 , retro_cjac_4180,
Microcebus murinus	ENSMICG00000005966	1 retrocopy	retro_mmur_31,