RetrogeneDB ID: retro_cjac_4182

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:66352101..66352958(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000013228
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MTCH1
• Ensembl ID: ENSCJAG00000005273
• Aliases: None
• Description: None

Sequence

>retro_cjac_4182
GGGGGGATGGCGGAAGCCAGAGCTCGCGGAGGTTGCAGCGGCGGGGGTCGAGGCCAGAGCTCGCGATCCACCGCTAGCGC
ACTGTGCACATCCGTGCCACCCTCGCTCAGCCCTTGGCCCACAGGATGGACGGCGGATCCGGGGGCCTGGGGTCTGGGGA
CAACGCCCCGACCACTGAGGCTCTTTTCGTGGCACTGGGCGTGGGCGTGACGGTGCTTAGCCATCCGCTGCTCTACATGA
AGCTGCTCATCCAGGTGTGTCATGAGCCGATGCCCCCTACCCTTGGGACCAATGTGCTGGGGAGGAAGGTCCTCTATCTG
CCAAGCTTCTTCACCTACGCCAAGTACATTGTGCAAGTGGATGGTAAGATAGGGCTGTTCCAAGGCCTGAGCCCCTGGCT
GATGTCCAACTCTCTCTCCACTGTGACCCGGGGTAGCATGAAGGTTTTCCCTACAGATGAGATCGAGCAGATTTCCAGCA
AGGATGACATGAAGACTTCCCTGAAGAAAGTTGTGAAGGAGACCTCCTATGAGATGATGATGCAGTGCGTGTCCCGCATG
TTGGCCCACCCACTGCATGTCATTTCAATGCGCTGCATGGTTCAGTTTGTGGAACGGGAGGCCAAGTACGGTGGTGTGCT
GACCTCCATTGGGAAGATTTTCAAAGAGGAAGGGCTGCTGGGATTCTTTGTTGGATTAATCCCTCACCTCCTGGGCGATG
TGGTTTTCTTGTGGGGCTGTAACCTGCTGGCCCACTTCATCAATGCCTACCTGGTAGATGACAGCTTCAGCCAGGCCCTG
GCTATCCCGAGCTATACCAAGTTCCTGATGGGGATCACAGTGAGCATACTGACCTAT

Alignment

ORF - retro_cjac_4182 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.32 %
• Parental protein coverage: 70.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GAGAGAGARGG-AAAGVEARARDPPPAHRAHPRHP-RPAAQPSARRMDGGSGGLGSGDNAPTTEALFVAL
          G..A.A.ARGG.AAAGVEARARDPP.AH.A...HP....AQP.A.RMDGGSGGLGSGDNAPTTEALFVAL
Retrocopy GGMAEARARGG>AAAGVEARARDPPLAHCA---HP>ATLAQPLAHRMDGGSGGLGSGDNAPTTEALFVAL

Parental  GAGVTALSHPLLYVKLLIQVGHEPMPPTLGTNVLGRKVLYLPSFFTYAKYIVQVDGKIGLFRGLSPRLMS
          G.GVT.LSHPLLY.KLLIQV.HEPMPPTLGTNVLGRKVLYLPSFFTYAKYIVQVDGKIGLF.GLSP.LMS
Retrocopy GVGVTVLSHPLLYMKLLIQVCHEPMPPTLGTNVLGRKVLYLPSFFTYAKYIVQVDGKIGLFQGLSPWLMS

Parental  NALSTVTRGSMKKVFPPDEIEQVSNKDDMKTSLKKVVKETSYEMMMQCVSRMLAHPLHVISMRCMVQFVG
          N.LSTVTRGSMK.VFP.DEIEQ.S.KDDMKTSLKKVVKETSYEMMMQCVSRMLAHPLHVISMRCMVQFV.
Retrocopy NSLSTVTRGSMK-VFPTDEIEQISSKDDMKTSLKKVVKETSYEMMMQCVSRMLAHPLHVISMRCMVQFVE

Parental  REAKYSGVLSSIGKIFKEEGLLGFFVGLIPHLLGDVVFLWGCNLLAHFINAYLVDDSFSQALAIRSYTKF
          REAKY.GVL.SIGKIFKEEGLLGFFVGLIPHLLGDVVFLWGCNLLAHFINAYLVDDSFSQALAI.SYTKF
Retrocopy REAKYGGVLTSIGKIFKEEGLLGFFVGLIPHLLGDVVFLWGCNLLAHFINAYLVDDSFSQALAIPSYTKF

Parental  VMGIAVSMLTY
          .MGI.VS.LTY
Retrocopy LMGITVSILTY

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	0.09 RPM	25.27 RPM
SRP051959_heart	0.05 RPM	28.15 RPM
SRP051959_kidney	0.00 RPM	35.01 RPM
SRP051959_liver	0.04 RPM	21.53 RPM
SRP051959_lung	0.03 RPM	29.82 RPM
SRP051959_lymph_node	0.23 RPM	16.00 RPM
SRP051959_skeletal_muscle	0.02 RPM	37.15 RPM
SRP051959_spleen	0.04 RPM	20.17 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4182 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4182 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4182 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005273	2 retrocopies	retro_cjac_2480, retro_cjac_4182 ,
Callithrix jacchus	ENSCJAG00000020213	3 retrocopies	retro_cjac_1551, retro_cjac_2003, retro_cjac_3812,