RetrogeneDB ID: retro_cjac_1380

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:16482176..16483025(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OTX2
• Ensembl ID: ENSCJAG00000018583
• Aliases: None
• Description: orthodenticle homeobox 2 [Source:HGNC Symbol;Acc:8522]

Sequence

>retro_cjac_1380
ATGATGTCTTATCTTAAGCAACCGCCTTACGCAGTCAATGGGCTGAGTCTGACCACTTCGGGTATGGGCTTGATGCATCC
CTCTGTGGGCTACCCGGCCACCCCCTGGAAACAGCGCTGGGAGAGGATGATGTTCACTCGGGCGCATCTAGATGTGCTGG
AAGCACTGTTTGCCAAGACCCAGTACCCAGACATCTTCATGCGAGGGGAGGTGGCACTGAAAATCAACTTGCCCGAGTCC
AGGGTGCAGGTATGGTTTAAGAATTGAAGAGCTAAGTGCCGCCAGCAACAACAACAACAGCAGAATGGAGGTCAAAACAA
AGTGAGACCTGCCAAAAAGAAGACCTCTCCAGCTTGGTCAGTGAGTTCCGAGAGTGGAGCAAGTGGCCAATTCACTCCCC
GCTCTAGCACCTCAGTCCCAACCATTGCCAGCAACAGTGCTCCTGTGTCTATCTGGAGCCCAGCTTCCATCTCCCCACTG
TCAGATCCCTTGTCCACCTCCTCTTCCTGCATACAGAGGTCCTATCCCATGACCTATACTCAGGCTTCAGGTTATAGTCA
AGGATATGCTGGCTCAACTTCCTACTTTGGGGGCATGGACTGTGGATCTTATTTGACTCCTATGCATCACCAGCTTCCCA
GACCAGGGGCCACACTCAGTCCCATGGGTACCAATGCAGTCACCAGCCATCTCAATCAGTCCCCAGCTTCTATTTCCACC
CAGGGATATGGAGCTTCAAGCTTGGGCTTTAACTCAACCACCGATTGCTTGGATTATAAGGACCGAACTGCCTCCTGGAA
GCTTACCTTCAATGCTGACTGCTTGGATTATAAAGATCAGGCATCCTCG

Alignment

ORF - retro_cjac_1380 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMSYLKQPPYAVNGLSLTTSGMDLLHPSVGYPVVPSRPR-PSPLTSRACFNPKKCDFLQIRYGEPQIFER
          MMSYLKQPPYAVNGLSLTTSGM.L.HPSVGYP..P...R.......RA........F....Y..P.IF.R
Retrocopy MMSYLKQPPYAVNGLSLTTSGMGLMHPSVGYPATPWKQRWERMMFTRAHLDVLEALFAKTQY--PDIFMR

Parental  TEVMAPIQRAHSKVQVWFKNRRAKCRQQQQQQQNGGQNKVRPAKKKTSPAREVSSESGTSGQFTPPSSTS
          .EV...I....S.VQVWFKN.RAKCRQQQQQQQNGGQNKVRPAKKKTSPA..VSSESG.SGQFTP.SSTS
Retrocopy GEVALKINLPESRVQVWFKN*RAKCRQQQQQQQNGGQNKVRPAKKKTSPAWSVSSESGASGQFTPRSSTS

Parental  VPTIASSSAPVSIWSPASISPLSDPLSTSSSCMQRSYPMTYTQASGYSQGYAGSTSYFGGMDCGSYLTPM
          VPTIAS.SAPVSIWSPASISPLSDPLSTSSSC.QRSYPMTYTQASGYSQGYAGSTSYFGGMDCGSYLTPM
Retrocopy VPTIASNSAPVSIWSPASISPLSDPLSTSSSCIQRSYPMTYTQASGYSQGYAGSTSYFGGMDCGSYLTPM

Parental  HHQLPGPGATLSPMGTNAVTSHLNQSPASLSTQGYGA-SLGFNSTTDCL-YKDQTASWKLNFHADCLDYK
          HHQLP.PGATLSPMGTNAVTSHLNQSPAS.STQGYGA.SLGFNSTTDCL.YKD.TASWKL.F.ADCLDYK
Retrocopy HHQLPRPGATLSPMGTNAVTSHLNQSPASISTQGYGASSLGFNSTTDCLDYKDRTASWKLTFNADCLDYK

Parental  DQTSS
          DQ.SS
Retrocopy DQASS

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	0.00 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.00 RPM
SRP051959_lymph_node	0.00 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.02 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1380 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1380 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1380 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014741	1 retrocopy	retro_btau_687,
Callithrix jacchus	ENSCJAG00000009866	1 retrocopy	retro_cjac_326,
Callithrix jacchus	ENSCJAG00000010981	1 retrocopy	retro_cjac_891,
Callithrix jacchus	ENSCJAG00000018583	1 retrocopy	retro_cjac_1380 ,
Cavia porcellus	ENSCPOG00000003420	1 retrocopy	retro_cpor_149,
Sus scrofa	ENSSSCG00000005063	1 retrocopy	retro_sscr_417,
Tursiops truncatus	ENSTTRG00000004650	1 retrocopy	retro_ttru_473,