RetrogeneDB ID: retro_cjac_4061

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:47316437..47317067(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAP2K2
• Ensembl ID: ENSCJAG00000015084
• Aliases: None
• Description: None

Sequence

>retro_cjac_4061
ATGCTGGCTTGGAGGAAGCCGGTGCTGCAGGTGCTCACCATCAACTCTGCCATCACCAAGGGCTCGTCCCCCGCCAGCGA
GGTGCCTCCGAGGCAAACCTGGTGGACCTGCATAAGAGGCTGAAGAAGCTGCAACTTGATGAGCAGCAGAAGAGGCTGGA
AGCCTTCCTCACCCAGAAAGCCAAGGTTGGCGAGCTCAAAGACGATTACTTCAAAAGGGTCTCAGAGCTGGGTGTGGACA
ACAGCAGGGTGGTCACCAAAGTCCAGCACAGACCCTCGGGACTCATCATGGCCAGGAAGCTGATCCACCTTGAAATCAAG
CCAGCCATCTGGAACCAGATCATCTGAGAACTGCAGGTCCTGCTCCAGTGCAACTTACCATACATCATGGGCTTCTAACG
GGGCTTTCTACAATGACAGGGAGATCAGCATCTGCATGGAGCACATGGTTGGTGGCTCCCTGGACCAGGTGCTGAAAAAG
GCCAAGAGGATTCCCGAGGAGATCCTGGGGAAAGTCAGCACTGTGGTCCTCTGGGGCTTGGGGTACCTCGGAGAGAAGCA
CCAGAATCATGCACAAGATGTGAAACCCTCCAACATCTTGGTGAACTCCAGAGGGGAGATCAAGCTGTGC

Alignment

ORF - retro_cjac_4061 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.81 %
• Parental protein coverage: 52.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLARRKPVLPALTINPAIAEGPSPTSE-GASEANLVDLQKKLEELELDEQQKKRLEAFLTQKAKVGELKD
          MLA.RKPVL..LTIN.AI..G.SP.SE.GASEANLVDL.K.L..L.LDEQQK.RLEAFLTQKAKVGELKD
Retrocopy MLAWRKPVLQVLTINSAITKGSSPASE<GASEANLVDLHKRLKKLQLDEQQK-RLEAFLTQKAKVGELKD

Parental  DDFERISELGAGNGGVVTKVQHRPSGLIMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGF-YGAFY
          D.F.R.SELG..N..VVTKVQHRPSGLIMARKLIHLEIKPAI.NQII.ELQVL..CN.PYI.GF..GAFY
Retrocopy DYFKRVSELGVDNSRVVTKVQHRPSGLIMARKLIHLEIKPAIWNQII*ELQVLLQCNLPYIMGF>NGAFY

Parental  SDGEISICMEHMDGGSLDQVLKEAKRIPEEILGKVSIAVLRGLAYLREKHQIMHRDVKPSNILVNSRGEI
          .D.EISICMEHM.GGSLDQVLK.AKRIPEEILGKVS..VL.GL.YL.EKHQ....DVKPSNILVNSRGEI
Retrocopy NDREISICMEHMVGGSLDQVLKKAKRIPEEILGKVSTVVLWGLGYLGEKHQNHAQDVKPSNILVNSRGEI

Parental  KLC
          KLC
Retrocopy KLC

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	17.82 RPM
SRP051959_heart	0.00 RPM	14.93 RPM
SRP051959_kidney	0.00 RPM	17.37 RPM
SRP051959_liver	0.00 RPM	15.81 RPM
SRP051959_lung	0.00 RPM	10.90 RPM
SRP051959_lymph_node	0.02 RPM	12.97 RPM
SRP051959_skeletal_muscle	0.00 RPM	23.65 RPM
SRP051959_spleen	0.00 RPM	12.14 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4061 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4061 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4061 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015084	1 retrocopy	retro_cjac_4061 ,
Equus caballus	ENSECAG00000009157	2 retrocopies	retro_ecab_668, retro_ecab_968,
Homo sapiens	ENSG00000126934	1 retrocopy	retro_hsap_3785,
Gorilla gorilla	ENSGGOG00000008832	1 retrocopy	retro_ggor_115,
Nomascus leucogenys	ENSNLEG00000003013	1 retrocopy	retro_nleu_1121,
Otolemur garnettii	ENSOGAG00000001658	1 retrocopy	retro_ogar_576,
Pan troglodytes	ENSPTRG00000010294	1 retrocopy	retro_ptro_2566,