RetrogeneDB ID: retro_cjac_1305

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:84384035..84384805(-)
• Located in intron of: ENSCJAG00000007770

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTRF1L
• Ensembl ID: ENSCJAG00000012787
• Aliases: None
• Description: None

Sequence

>retro_cjac_1305
TCAGAAGAAACAGATGAAAATGATTTGATCCTGGAAGTAATTGCAGGATTTGGAGGTCAGGAGGCAATGCTGTTTACTTC
AGAGATGTTTGATATGTATCAGTGATATGCTGCATTTAAAAGATGGCATTTTGAAACCCTGGAATATTTTCCAAGTGAAA
TAGGTGGCCTTAGACATGCATCTGCCAGCATTGGGGGTTCAGAAGCCTATAAGCATATGAAGTTTGAAGGAGGTGTGCAC
AGAGTACAAAGGGTGCCAAAGACAGAAAAGCGAGTTTGTATCCATACTAGCACCGTGACTGTAGCAATATTACCCCAACC
TACTGAGGTGAATCTGGTGATTAATCCAAAAGGTTTGAGAATTGACACTAAGTGAGCCAGTGGAGCTGGGGGGCAGCATG
TAAACACCACAGACAGTGCTGTCCGGATAGTTCATCTTCCAAAAGGTGTTGTTTCTGAATGTCAACAAGAGAGCTCTCAA
CTGAAAAATAAAGAGCTGGCTATGAAGAAGTTACGTGCAAATCTGTACAGCATGCATCTAGAAGAAACAAATAAGAGAGA
CAATGCTAGAAAAATTCAGATTGGAAGTAAAGGAAGATCGAGAAAATAAGAACTTATAATTTTCCACAGAACTGGGTCAC
AGATCACAGAATAAGCAAGTCACTGCATGATCTTCAAACTTTTACGCAAGGGGATTATCTACTGGATGAACTTGTACAGT
CATTGAAGGAATATGCTGATTATGAATCTTTAGTAGAAATTATTTCCCAA

Alignment

ORF - retro_cjac_1305 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.05 %
• Parental protein coverage: 67.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SEETDENDLILEVTAGVGGQEAMLFTSEMFDMYQRYAAFKRWHFETLEYFPSEIGGLRHASASIGGSEAY
          SEETDENDLILEV.AG.GGQEAMLFTSEMFDMYQ.YAAFKRWHFETLEYFPSEIGGLRHASASIGGSEAY
Retrocopy SEETDENDLILEVIAGFGGQEAMLFTSEMFDMYQ*YAAFKRWHFETLEYFPSEIGGLRHASASIGGSEAY

Parental  RHMKFEGGVHRVQRVPKTEKQGRIHTSTMTVAILPQPTEINLVINPKDLRIDTKRASGAGGQHVNTTDSA
          .HMKFEGGVHRVQRVPKTEK...IHTST.TVAILPQPTE.NLVINPK.LRIDTK.ASGAGGQHVNTTDSA
Retrocopy KHMKFEGGVHRVQRVPKTEKRVCIHTSTVTVAILPQPTEVNLVINPKGLRIDTK*ASGAGGQHVNTTDSA

Parental  VRIVHLPTGVVSECQQERSQLKNKELAMKKLRAKLYSMHLEEETNKRDNARKIQIGSKGRS-EKIRTYNF
          VRIVHLP.GVVSECQQE.SQLKNKELAMKKLRA.LYSMHL.EETNKRDNARKIQIGSKGRS.EKIRTYNF
Retrocopy VRIVHLPKGVVSECQQESSQLKNKELAMKKLRANLYSMHL-EETNKRDNARKIQIGSKGRS<EKIRTYNF

Parental  PQNRVTDHRISKSLHDLQTFMQGDYLLDELVQSLKEYADYESLVEIISQ
          PQN.VTDHRISKSLHDLQTF.QGDYLLDELVQSLKEYADYESLVEIISQ
Retrocopy PQNWVTDHRISKSLHDLQTFTQGDYLLDELVQSLKEYADYESLVEIISQ

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	6.48 RPM
SRP051959_heart	0.00 RPM	6.79 RPM
SRP051959_kidney	0.02 RPM	9.03 RPM
SRP051959_liver	0.00 RPM	5.42 RPM
SRP051959_lung	0.02 RPM	6.91 RPM
SRP051959_lymph_node	0.00 RPM	9.98 RPM
SRP051959_skeletal_muscle	0.02 RPM	5.68 RPM
SRP051959_spleen	0.00 RPM	7.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1305 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1305 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1305 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012787	1 retrocopy	retro_cjac_1305 ,
Homo sapiens	ENSG00000112031	1 retrocopy	retro_hsap_3018,
Sarcophilus harrisii	ENSSHAG00000017997	1 retrocopy	retro_shar_129,
Ictidomys tridecemlineatus	ENSSTOG00000009980	1 retrocopy	retro_itri_335,
Tupaia belangeri	ENSTBEG00000003131	2 retrocopies	retro_tbel_2448, retro_tbel_4085,