RetrogeneDB ID: retro_cjac_1658

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:2590374..2591086(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TERF1
• Ensembl ID: ENSCJAG00000007714
• Aliases: None
• Description: None

Sequence

>retro_cjac_1658
TCCGAGGACCCTCGCCCAACCTGCGACAGCGCCGAGGCTGTTCTTCACGGACTGTCGAGTCCAACCGCTTATCGATTGAG
AACTGTATACATGTGTCAGTTTTTGACAAGAATTGCAGCAGGAAAAAACTTGGATGCACAGTTTGAAAATGACGAACGAA
TTGGAACAGCCCTGATGAGCTGGGGTTCAATTGAAAAGGAAAAGGACGAACTTCACGAAGAAATACAGAATTTAATAGAA
ACTGAGGCTATCGCTGTTTGTATGGAAAATGGGCAACTTTAAAGAAGCAGAAGTCTTTGAAAGAATATTTGGTGATCCAA
ATTCTTACATGCCTTTAAAAAGGAAATTGCTTATGATAATCTCTCAGAAAGATACGTTTCATTACTTTTTTTCAACACTT
CAGCTACAACTGCATGATGGAGAAAATGAAGAGTTATGTGAATTATGTGCTAAGTGAAAAATCATCCACCTTTCTAATGA
AGGCAGCAGCAAAAGCCTAGAAAGTAAAAGAGCAAGAACAATAACTTCTCAAGACAAACCCAATGGTAATGATGTTGAAA
TGGAAACTGAAGCTAATTTGGATACAAGAAAAAGGTCGCACGAGAATCTTTTCTTATCTAGGTTGAAACATGGAACCCAG
CAACGAGACCTTCATAAGAAAGAAATAAAGAAGAGTAGGAACTCTTCAAAGTGCGAGAAAGAAAAAAGAAAG

Alignment

ORF - retro_cjac_1658 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.51 %
• Parental protein coverage: 58.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SEDFRQTRDSAEAIIHGLSSLTAYQLRTVYICQFLTRIAAGKNLDAQFENDERITPLESALMIWGSIEKE
          SED.R.T.DSAEA..HGLSS.TAY.LRTVY.CQFLTRIAAGKNLDAQFENDERI.....ALM.WGSIEKE
Retrocopy SEDPRPTCDSAEAVLHGLSSPTAYRLRTVYMCQFLTRIAAGKNLDAQFENDERI---GTALMSWGSIEKE

Parental  HDKLHEEIQNLIEVQAIAVCMEN-GNFKEAEEVFERIFGDPNSCAPLKRKLLMIISQKDTYH-SVFQHFS
          .D.LHEEIQNLIE..AIAVCMEN.GNFKEA.EVFERIFGDPNS..PLKRKLLMIISQKDT.H...FQHFS
Retrocopy KDELHEEIQNLIETEAIAVCMEN>GNFKEA-EVFERIFGDPNSYMPLKRKLLMIISQKDTFH>TFFQHFS

Parental  YNHMMEKVKSYVNDVLSEKSSTFLMKAAAKV-VESKRARTTTSQDKPNGNDVEMETEANLDTRKRSHKNL
          YN.MMEK.KSYVN.VLSEKSSTFLMKAAAK...ESKRART.TSQDKPNGNDVEMETEANLDTRKRSH.NL
Retrocopy YNCMMEKMKSYVNYVLSEKSSTFLMKAAAKA<LESKRARTITSQDKPNGNDVEMETEANLDTRKRSHENL

Parental  FLSKLKHGTQQRELNKERRVGTLQSAKRKKESRR
          FLS.LKHGTQQR.L.K........S.K..KE.R.
Retrocopy FLSRLKHGTQQRDLHKKEIKKSRNSSKCEKEKRK

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	0.11 RPM	4.50 RPM
SRP051959_heart	0.11 RPM	6.03 RPM
SRP051959_kidney	0.04 RPM	6.15 RPM
SRP051959_liver	0.22 RPM	3.51 RPM
SRP051959_lung	0.11 RPM	6.30 RPM
SRP051959_lymph_node	0.25 RPM	7.26 RPM
SRP051959_skeletal_muscle	0.02 RPM	2.73 RPM
SRP051959_spleen	0.29 RPM	5.44 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1658 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1658 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1658 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002407	1 retrocopy	retro_chof_944,
Callithrix jacchus	ENSCJAG00000007714	1 retrocopy	retro_cjac_1658 ,
Homo sapiens	ENSG00000147601	6 retrocopies	retro_hsap_1166, retro_hsap_1917, retro_hsap_2493, retro_hsap_3099, retro_hsap_4324, retro_hsap_4861,
Oryctolagus cuniculus	ENSOCUG00000002793	1 retrocopy	retro_ocun_546,
Pan troglodytes	ENSPTRG00000022919	7 retrocopies	retro_ptro_1245, retro_ptro_1445, retro_ptro_2095, retro_ptro_3236, retro_ptro_3241, retro_ptro_611, retro_ptro_802,