RetrogeneDB ID: retro_cjac_2480

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:139224335..139225072(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000034082
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_2480
CCAAACACAAAGCCTTATGTGCTGGGGAGGAAAGCCCTCTATCTGCCAATCTTCTTCATCTACACCAAGTACACTGTGCA
AGTGGATGCTATGATACGGCTTTTCCAAGGCCTGAACCCCTGGTTGATGTCCAGTGCCCTTTCCACTGTGACCTGGGGTA
GCTTGAAGAAGGTTTTCCCTCTGGATGAGATTGAGCAGGTTTCCAACAAGGATGATATGAAGATTTTGCTGAAGAAAGTT
GTGAAGGAGACCTCCTACGAGATGATGATGCAGTGCGTGTCCGCATGTTGGCCCACCCGCTGCGTGTCATTTCAATGCGC
TGCATGGTCCAGTTTGTGGGATGGGAAGCCAAATACAGTGGTGTGCTGAGCTCCATTGGGAAGACTTTTCAAAGAGGAAG
GGCTGCTGGGTGGGATTTGTTGGATTAATCCCTTACCTCCTTAATTTGTTGGGCAATGTGGTTTTTTTGTGGGGCCGTAA
CCTGCTGGCCCACTTCATCAGTGCCTACCTGGTGGATGACAGCTTCTGCCAGGCCCTGGCCATCCAGGGCCACACCAAGT
ATATGATGGGGATTGCAGTGAGCATGCTGACCTACCCCTTCCTGCTAGTTGGCAACCTGCAGGCTGGGCTCCCCTGTTAC
TTGCCGGTGTTCAAATCCTGGATTCACTGCTGGAAGTACTTGAATATAAAGGGCCAGCTCTTCTGAGACTCCAACCTGCT
TCTCCACTGGGTGTCAT

Alignment

ORF - retro_cjac_2480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.04 %
• Parental protein coverage: 60.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PTLGTNVLGRKVLYLPSFFTYAKYIVQVDGKIGLFRGLSPRLMSNALSTVTRGSMKKVFPPDEIEQVSNK
          P.....VLGRK.LYLP.FF.Y.KY.VQVD..I.LF.GL.P.LMS.ALSTVT.GS.KKVFP.DEIEQVSNK
Retrocopy PNTKPYVLGRKALYLPIFFIYTKYTVQVDAMIRLFQGLNPWLMSSALSTVTWGSLKKVFPLDEIEQVSNK

Parental  DDMKTSLKKVVKETSYEMMMQCVS-RMLAHPLHVISMRCMVQFVGREAKYSGVLSSIGK-IFKEEGLLG-
          DDMK..LKKVVKETSYEMMMQCVS.RMLAHPL.VISMRCMVQFVG.EAKYSGVLSSIGK..FKEEGLLG.
Retrocopy DDMKILLKKVVKETSYEMMMQCVS<RMLAHPLRVISMRCMVQFVGWEAKYSGVLSSIGK>LFKEEGLLG>

Parental  FFVGLIPHLL---GDVVFLWGCNLLAHFINAYLVDDSFSQALAIRSYTKFVMGIAVSMLTYPFLLVGDLM
          .FVGLIP.LL...G.VVFLWG.NLLAHFI.AYLVDDSF.QALAI...TK..MGIAVSMLTYPFLLVG.L.
Retrocopy GFVGLIPYLLNLLGNVVFLWGRNLLAHFISAYLVDDSFCQALAIQGHTKYMMGIAVSMLTYPFLLVGNLQ

Parental  AVNNCGLQAGLPPYSPVFKSWIHCWKYLSV-QVSKYWTEEAFPVVCH
          A....GL...LP........W....KYL.....S...T...F...CH
Retrocopy A----GLPCYLPVFKSWIHCW----KYLNI>RASSSETPTCFSTGCH

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	0.98 RPM	25.27 RPM
SRP051959_heart	0.25 RPM	28.15 RPM
SRP051959_kidney	1.58 RPM	35.01 RPM
SRP051959_liver	2.51 RPM	21.53 RPM
SRP051959_lung	0.63 RPM	29.82 RPM
SRP051959_lymph_node	0.27 RPM	16.00 RPM
SRP051959_skeletal_muscle	0.39 RPM	37.15 RPM
SRP051959_spleen	0.78 RPM	20.17 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2480 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2480 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2480 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3671
Pan troglodytes	retro_ptro_2490
Gorilla gorilla	retro_ggor_2481
Pongo abelii	retro_pabe_3011

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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,