RetrogeneDB ID: retro_cjac_4195

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:83992919..83993552(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022740
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAD2L2
• Ensembl ID: ENSCJAG00000013267
• Aliases: None
• Description: MAD2 mitotic arrest deficient-like 2 (yeast) [Source:HGNC Symbol;Acc:6764]

Sequence

>retro_cjac_4195
ATGACCACGCTTACACGGCAGGACCTCAACTTTGGCCAAGTGGTGGCCGATGTGCTCTGCGAGTTTCTGGAGGTGGCTGT
GCATCTCATCCTCTACGTGCACGAGGTCTACCCGGTGGGCATTTTCCAGAAACGTAAGAAGTACAACGTGCCGGTCCAGA
TGTCCTGCCACCCGGAGCTGAATCAGTATATCCAGGATACGCTGCACTGCGTCAAGCCACTCCTGGAGAAGAATGATGTG
GAGAAAGTGGTGGTGGTGATTTTGGATAAAGAGCACCGCCCAGTGGAGAAATTCGTCTTTGAGATCACCCAGCCTCCACT
GCTATCCATCAGCTCAGACTCCCTTTTGTCTCACGTGGAGCAGCTGCTCCGAGCCTTCATCCTGAAGATCAGCGTGTGCG
ATGCTGTCCTGCACCACAATGCCCTAGGCTGTACCTTCACAGTCCTGGTGCACACGAGAGAAGCTGCCACTCGCAACATG
GAGAAAATCCAGGTCATCAAGGATTTCCCCTGGATCCTGGCAGATGAGCAGGATGTCCACATGCATGACCCCCGGCTGAT
ACCACTGAAAACCATGACGTCGGACATTTTAAAGATGCAGCTTTACGTGGAAGAGCGCGCCCATAAAGGCAGC

Alignment

ORF - retro_cjac_4195 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTTLTRQDLNFGQVVADVLCEFLEVAVHLILYVREVYPVGIFQKRKKYNVPVQMSCHPELNQYIQDTLHC
          MTTLTRQDLNFGQVVADVLCEFLEVAVHLILYV.EVYPVGIFQKRKKYNVPVQMSCHPELNQYIQDTLHC
Retrocopy MTTLTRQDLNFGQVVADVLCEFLEVAVHLILYVHEVYPVGIFQKRKKYNVPVQMSCHPELNQYIQDTLHC

Parental  VKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSISSDSLLSHVEQLLRAFILKISVCDAVLDHN
          VKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSISSDSLLSHVEQLLRAFILKISVCDAVL.HN
Retrocopy VKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSISSDSLLSHVEQLLRAFILKISVCDAVLHHN

Parental  PPGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVHMHDPRLIPLKTMTSDILKMQLYVEERAHKG
          ..GCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVHMHDPRLIPLKTMTSDILKMQLYVEERAHKG
Retrocopy ALGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVHMHDPRLIPLKTMTSDILKMQLYVEERAHKG

Parental  S
          S
Retrocopy S

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	0.04 RPM	3.79 RPM
SRP051959_heart	0.18 RPM	5.84 RPM
SRP051959_kidney	0.47 RPM	9.34 RPM
SRP051959_liver	0.24 RPM	5.89 RPM
SRP051959_lung	0.15 RPM	5.40 RPM
SRP051959_lymph_node	0.00 RPM	5.71 RPM
SRP051959_skeletal_muscle	0.15 RPM	4.26 RPM
SRP051959_spleen	0.06 RPM	4.77 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4195 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4195 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4195 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	ENSCJAG00000013267	1 retrocopy	retro_cjac_4195 ,