RetrogeneDB ID: retro_cjac_1359

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:84571556..84572939(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TBL3
• Ensembl ID: ENSCJAG00000015245
• Aliases: None
• Description: None

Sequence

>retro_cjac_1359
GCACTGCAGGATCCGTCGTGCCTGGCTGTGCTGACTGCCCACTACAGCACTGTCACCTCACTGGCTTTCAGTGCCGACGG
CCACACTATGCTCAGCTCCGGCTGTGACAAGATCTGTATCATCTGGGACCTTCAGAGCCACCAGGCCACGAGGACTGTGC
TGGTGTTTGAGAACGTGGAGACCGCTGTGCTGTTGCCAGAGGAGCTGGCATCTGAGCTGGGTATGAAGTCCCCAGGCCTG
CACTTCCTGACAGCTGGCGACCAAGGCACTCTGCGCGTGTGGGAGGCAGCTTCTGGGCAGTGTGTGTACACGCAGGCCCG
GCCGCCGGGCCCTGGGCGGGAGCTGACCCACTGCACCCTGGCCCGCACCGCCGGCCTGCTCCTCAGCGCCACTGCCGACC
ATGACCTGCTGCTCTACGAGGCTCACTCCCCGCGGCTGCAGAAACAGTGCACTGGCTATAGTGAGGAGGTCCTGGATGCC
CGGTTTCTTGGGTCTCAGGACTCCCACATCAGCGTGGCCTCCAATAGCCCCTGCCTGACAGTGTTTGAGCTACAGACATC
AGCCTGCCAGATCCTCCATGGCCACAGGGATATCGTTCTGGCTCTGGACGTGTTCCGGAAGGGGTGGCTCTTTGCCAGCT
GTGCCAAGGATCAGAGTGTCCGAATCTGGAGGATGAACAAGGCTGGCCAGGTGGTCTGCATGACTCAGGGTTCCGGCCAT
ATGCACAGTGTCGGCACCATCTGCTGCTCTAGGCTGAAGGAGCCCTTCCTGGTGACGGGCAGCCAGGACTGCACTGTGAA
GCTGTGGCCTCCTCCCAAAGCCCTGCTGTCTAAGAACACAGCCCCAGACAGTGGCCCTGTCCTCCTGCAGGCCCAGAACA
CTCAGCGTTGCCACGATAAGGATATCAACAGCGTGGCCACTGCCCCCAACGACAAGCTGTTGGCCACGGGCTCATAGGAA
CGCATGGCCAAGCTCTGGGCCCTGTCACAGTGCCAGCTGCTGGGTGTCTTCTCAGGCCACCGGCACGGCCTCTGGTGTGT
CCAGTTCTCTCCCACGGACCAGGTGCCGGCCACAGCCTCAGCTGACGGCACCATCAAGCTCTGGGCGCTCTAGGACTTCA
GCTGTCTCAAGACATTTGAGGGACACGATGCTTCCATGCTGAAGGTGGCCTTTGTGAGCTGGGGCACACAGCTGCTGTCC
AGCGGCTCAGATGGCCTTGTGAAGCTCTGGACCATCAAGAACAACGAGTGTGTGCAGACGCTGGATGCCCACGATGACAA
GGCCTGGGGGCCGCACCACAGCCAGCTGGATGACCGCACCCTCACTGGCGCCAGCGACTCCCAAGTCATCCTCTGGAAGG
ATGTGACCAAGGAGGAGCAGGCC

Alignment

ORF - retro_cjac_1359 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.94 %
• Parental protein coverage: 57.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLQDRSCLAVLTAHYSAVTSLAFSADGHTMLSSGRDKICIIWDLQSHQAVRTVPVFESVETAVLLPEEPA
          .LQD.SCLAVLTAHYS.VTSLAFSADGHTMLSSG.DKICIIWDLQSHQA.RTV.VFE.VETAVLLPEE.A
Retrocopy ALQDPSCLAVLTAHYSTVTSLAFSADGHTMLSSGCDKICIIWDLQSHQATRTVLVFENVETAVLLPEELA

Parental  SELGVKSPGLHFLTAGDQGTLRVWEAASGQCVYTQARPPGPGRELTHCTLARTAGLLLSATADHNLLLYE
          SELG.KSPGLHFLTAGDQGTLRVWEAASGQCVYTQARPPGPGRELTHCTLARTAGLLLSATADH.LLLYE
Retrocopy SELGMKSPGLHFLTAGDQGTLRVWEAASGQCVYTQARPPGPGRELTHCTLARTAGLLLSATADHDLLLYE

Parental  ARSLRLQKQFAGYSEEVLDVRFLGPEDSHIIVASNSPCLKVFELQTSACQILHGHTDIVLALDVFRKGWL
          A.S.RLQKQ..GYSEEVLD.RFLG..DSHI.VASNSPCL.VFELQTSACQILHGH.DIVLALDVFRKGWL
Retrocopy AHSPRLQKQCTGYSEEVLDARFLGSQDSHISVASNSPCLTVFELQTSACQILHGHRDIVLALDVFRKGWL

Parental  FASCAKDQSVRIWRMNKAGQVVCVAQGPGHTHSVGTVCCSRLKESFLVTGSQDCTVKLWPLPKALLSKNT
          FASCAKDQSVRIWRMNKAGQVVC..QG.GH.HSVGT.CCSRLKE.FLVTGSQDCTVKLWP.PKALLSKNT
Retrocopy FASCAKDQSVRIWRMNKAGQVVCMTQGSGHMHSVGTICCSRLKEPFLVTGSQDCTVKLWPPPKALLSKNT

Parental  APDSGPVLLQPQTNQRCHDKDINSVAIAPNDKLLATGSQDRTAKLWALPQCQLLGVFSGHRRGLWCVQFS
          APDSGPVLLQ.Q..QRCHDKDINSVA.APNDKLLATGS..R.AKLWAL.QCQLLGVFSGHR.GLWCVQFS
Retrocopy APDSGPVLLQAQNTQRCHDKDINSVATAPNDKLLATGS*ERMAKLWALSQCQLLGVFSGHRHGLWCVQFS

Parental  PMDQVLATASADGTIKLWALQDFSCLKTFEGHDASVLKVAFVSRGTQLLSSGSDGLVKLWTIKNNECVRT
          P.DQV.ATASADGTIKLWAL.DFSCLKTFEGHDAS.LKVAFVS.GTQLLSSGSDGLVKLWTIKNNECV.T
Retrocopy PTDQVPATASADGTIKLWAL*DFSCLKTFEGHDASMLKVAFVSWGTQLLSSGSDGLVKLWTIKNNECVQT

Parental  LDAHDDKVWGLHCSRLDDCALTGASDSRVILWKDVTEAEQA
          LDAHDDK.WG.H.S.LDD..LTGASDS.VILWKDVT..EQA
Retrocopy LDAHDDKAWGPHHSQLDDRTLTGASDSQVILWKDVTKEEQA

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	4.81 RPM
SRP051959_heart	0.00 RPM	5.42 RPM
SRP051959_kidney	0.02 RPM	6.28 RPM
SRP051959_liver	0.00 RPM	4.77 RPM
SRP051959_lung	0.00 RPM	5.35 RPM
SRP051959_lymph_node	0.00 RPM	6.53 RPM
SRP051959_skeletal_muscle	0.02 RPM	9.96 RPM
SRP051959_spleen	0.00 RPM	3.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1359 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1359 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1359 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	ENSCJAG00000015245	1 retrocopy	retro_cjac_1359 ,