RetrogeneDB ID: retro_cjac_4102

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:95177833..95179316(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STAU1
• Ensembl ID: ENSCJAG00000016233
• Aliases: None
• Description: None

Sequence

>retro_cjac_4102
GAAAGCATAACCCCTACCGTAGAACTAAATGCACTGTGCATGAAACTTGGAAAAAAACCAATATATAAGCCTGTTGACCC
TTACTCTCTGATGCAATCCACCTATAACTACAACATGAGAGGAGGTGTTTATCCCCTGAGGTACTTTTACCCATTTCCAG
TTCCACCTTTACTTTATCAAGTGGAGCTTTCTGTGGGAGGACAGCAATTTAATGGGAAAGGAAAGACAAGACAGGCTGCA
AAACATACTGCTGCTGCCAAAGCGTTGAGGATCCTGCAGAATGAGCCCCCACCAGAGAGGATGGAGGTGAATGGAAGAGA
ATCAGAAGAAAATCTCAATAAATCTGAAATAAGTCAAGTGTTTGAGATTGCACTTAAATGAAACTTGCCTGTGAATTTTG
AGGTGGCCTGGGAGAGTGGCGCACCCCACATGAAGGATTCTGTGACCAAGGTTTCGGTTGGGGAGTTTGTGGAGGAAGGT
GAAGGGAAAAGCAAGAAGATTTCAAAGAAAAATGCCGCCATAACTGTCCTTGAGGAGCTGAAGAAGTTACCGCCCCTGCC
TGCAGTTGAACAAGTAAAGCCTAGAATCAAAAAGAAAACAAAACCTATAGTAAAGCCACAGACAACCCCAGAATATGGCC
AGGGGATCTATCGGATTAGCAGACTGGCCCAGATCCAGCAGGCAAAAAAGGAGAGGGAGCTAGAGTACATGCTTCTCACA
GAGCTAGGCCTTCCATGCCACAGGGAGTTCGCAATGCAGGTAAAGGTTGGAAACCACACTGCAGAAGGAACAGGCACCAA
CAAGAAGGTGGCCAGGTGCAATGCAGCTGAGAACATGCTGGAGGTCCTTGGTCTCAAAGTCCCGCAGGCACAGCCCACCA
AGCCAGCACTCAAGTCAGAGGAGAAGACACCCATAAAGAAACGAGGGGATGGAAGAAAAGTAACCTTTTTTGAACCTGGC
TCTGGGGATGAAAATGGGACTAGTAATAAAGAGGATGAGTTCAAGATGCCTTATCTAAGTCATCAGCAGCTGCCTGCTGG
AATTCTTCCCATGGTGCCCGAGGTCGCTCAGGCTGTAGGAGTTAGTCAAGGACATCACACCAAAGATTTCACCAGGGCAG
CTCCCAATCCTTCCAGGGCCACAGTAACTGCCATGATAGCCCGAGAGTTGTTGTATGGGGGCACCTCGCCCATAGCCAAG
ACCATTTTAAAGAATAACATCTCTTCAGGCCATGTACCCCATGGACCTCACAAGACCCTCTGAGGAACTGGACTATCTTT
TCAGAGTTTAGGGATTTCAGGTTGACTACAAAGACTTCCCCCAAAACAACAAGAATGAATTTGTATCTCTTATCAATTGC
TCCTCTCAGCCGTCTCTGATCAGCCATGGTATTGGCAAGGATGTGGAGTCCTGCCATGATATGGCTGCACTGAACATCTT
AAAGTTGTTGTCTGAGTTGGACCAACAAAGTACAGAGATGCCT

Alignment

ORF - retro_cjac_4102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.76 %
• Parental protein coverage: 85.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ESITPTVELNALCMKLGKKPMYKPVDPYSRMQSTYNYNMRGGAYPPRYFYPFPVPPLLYQVELSVGGQQF
          ESITPTVELNALCMKLGKKP.YKPVDPYS.MQSTYNYNMRGG.YP.RYFYPFPVPPLLYQVELSVGGQQF
Retrocopy ESITPTVELNALCMKLGKKPIYKPVDPYSLMQSTYNYNMRGGVYPLRYFYPFPVPPLLYQVELSVGGQQF

Parental  NGKGKTRQAAKHDAAAKALRILQNEPPPERLEVNGRESEEENLNKSEISQVFEIALKRNLPVNFEVARES
          NGKGKTRQAAKH.AAAKALRILQNEPPPER.EVNGRESEE.NLNKSEISQVFEIALK.NLPVNFEVA.ES
Retrocopy NGKGKTRQAAKHTAAAKALRILQNEPPPERMEVNGRESEE-NLNKSEISQVFEIALK*NLPVNFEVAWES

Parental  GPPHMKNFVTKVSVGEFVGEGEGKSKKISKKNAAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTT
          G.PHMK..VTKVSVGEFV.EGEGKSKKISKKNAAI.VLEELKKLPPLPAVE.VKPRIKKKTKPIVKPQTT
Retrocopy GAPHMKDSVTKVSVGEFVEEGEGKSKKISKKNAAITVLEELKKLPPLPAVEQVKPRIKKKTKPIVKPQTT

Parental  PEYGQGINPISRLAQIQQAKKEKEPEYMLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENM
          PEYGQGI..ISRLAQIQQAKKE.E.EYMLLTE.GLP..REF.MQVKVGNHTAEGTGTNKKVA..NAAENM
Retrocopy PEYGQGIYRISRLAQIQQAKKERELEYMLLTELGLPCHREFAMQVKVGNHTAEGTGTNKKVARCNAAENM

Parental  LEILGFKVPQAQPTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGIL
          LE.LG.KVPQAQPTKPALKSEEKTPIKK.GDGRKVTFFEPGSGDENGTSNKEDEF.MPYLSHQQLPAGIL
Retrocopy LEVLGLKVPQAQPTKPALKSEEKTPIKKRGDGRKVTFFEPGSGDENGTSNKEDEFKMPYLSHQQLPAGIL

Parental  PMVPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSGHVPHGP-LT
          PMVPEVAQAVGVSQGHHTKDFTRAAPNP..ATVTAMIARELLYGGTSP.A.TILKNNISSGHVPHGP...
Retrocopy PMVPEVAQAVGVSQGHHTKDFTRAAPNPSRATVTAMIARELLYGGTSPIAKTILKNNISSGHVPHGP<SQ

Parental  RPSEQLDYLSRVQGFQVEYKDFPK-NNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSEL
          .P.......S....F....K..PK.NNKNEFVSLINCSSQP.LISHGIGKDVESCHDMAALNILKLLSEL
Retrocopy DPLRNWTIFSEFRDFRLTTKTSPK<NNKNEFVSLINCSSQPSLISHGIGKDVESCHDMAALNILKLLSEL

Parental  DQQSTEMP
          DQQSTEMP
Retrocopy DQQSTEMP

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	0.07 RPM	35.17 RPM
SRP051959_heart	0.00 RPM	37.34 RPM
SRP051959_kidney	0.04 RPM	50.12 RPM
SRP051959_liver	0.02 RPM	34.87 RPM
SRP051959_lung	0.03 RPM	41.64 RPM
SRP051959_lymph_node	0.02 RPM	25.84 RPM
SRP051959_skeletal_muscle	0.02 RPM	28.83 RPM
SRP051959_spleen	0.08 RPM	33.47 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4102 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4102 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4102 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016233	1 retrocopy	retro_cjac_4102 ,
Monodelphis domestica	ENSMODG00000016276	1 retrocopy	retro_mdom_1931,
Sus scrofa	ENSSSCG00000027444	1 retrocopy	retro_sscr_233,