RetrogeneDB ID: retro_cjac_3563

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01184653.1:9484..10560(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000002166
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SF3A2
• Ensembl ID: ENSCJAG00000013206
• Aliases: None
• Description: None

Sequence

>retro_cjac_3563
ATGGACTTCTAGCATCGCCCTGGGGGCAAGACTGGGAGGGGAGGGCGTGACTTCCTCCAAGAGCAATGGTGACTGCAGGG
AGCGCCTCCGGCAGCTGGCCCTGGAGACCATCGACATCAACAAGGACCCATATTTTATGAAAAACCACCTGGGCTCCTAT
GAATGCAAGCTCTGCCTGACGTTTCACGACGAGGGGAGCTACCTGGCACATACCCAGGGGAAGAAGCACAAGACCAACTT
GGCCCAGCAAGCAGCCAAGGATGCCAAGGAGGCCCCTGCCCAGCCTGCGCCTGAGAAGGTCAAGGTGGAGGTGAAGAAGT
TTGTGAAGATCGGCCACCCGGGCTACAAAGTGGCCAAGCAGAGGGACTCAGAGATGGGCCAGCAGAGCCTCCTCTTCCAG
ATCGACTACGCTGAGATCGCCGAGGGCATCATGCTGCGCCACCGCTTCACGTCTGCTTACGAGCCACAGCTCCAGCCCCC
GGACTGGCTCTGGCAGTACCTGCTGATGGCTGCCAAGACCTATGAGACCATCACCTTCAAGGTGCTGAGCAGAGAGATCG
ACAAGGCAGAGGACAAGTTCTGGACTCACTGGAACCGGGAGACCAAGCAGTTCTTTCTCCAGTTCCACTTTAAGATGCAG
AAGCCCCCGGCTCCACCCACCCTCCCCACCGGGCCCCCTGGGGTGAAGCGGCCTCCACCCCCACTGATGACCAGTCTGCC
CCCTCGGCCACCGCTGCCCGAGTCTTTACCACCGCCCCCGCCAGGAGGCCTGCCTCTGCCACCCATGCCCCCCCATGAGG
CCTGCACCCTCAGGGCCCCCAGGACCACCCCAGCTGCCCCCACCAGCTCCACGGGTTCACCCACTGGCCCCAGTGGTGCA
CCCTGCCACATCTGGGGTCCATCCCCCAGCTCCTGGGGTTCACCCCCCAGCTCCTGGCGTCCATCCCCCAGCCCCTGTGG
TCCACCCACCAACCTCTGGGGTCCATCCCCCAGCTCCTGGAGTTCACACTCCAGCCCCTGGGGTTCACCCACCAGCCCCT
GGAGTCCACCCACCAGCCCCGGGGGTCCACCCTCCC

Alignment

ORF - retro_cjac_3563 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.85 %
• Parental protein coverage: 77.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDFQHRPGGKTGSG-GVASSSESNRDRRERLRQLALETIDINKDPYFMKNHLGSYECKLCLTLHNNEGSY
          MDF.HRPGGKTG.G.GV..SS.SN.D.RERLRQLALETIDINKDPYFMKNHLGSYECKLCLT.H..EGSY
Retrocopy MDF*HRPGGKTGRG>GV-TSSKSNGDCRERLRQLALETIDINKDPYFMKNHLGSYECKLCLTFHD-EGSY

Parental  LAHTQGKKHQTNLARRAAKEAKEAPAQPAPEKVKVEVKKFVKIGRPGYKVTKQRDSEMGQQSLLFQIDYP
          LAHTQGKKH.TNLA..AAK.AKEAPAQPAPEKVKVEVKKFVKIG.PGYKV.KQRDSEMGQQSLLFQIDY.
Retrocopy LAHTQGKKHKTNLAQQAAKDAKEAPAQPAPEKVKVEVKKFVKIGHPGYKVAKQRDSEMGQQSLLFQIDYA

Parental  EIAEGIMPRHRFMSAYEQRIEPPDRRWQYLLMAAEPYETIAFKVPSREIDKAEGKFWTHWNRETKQFFLQ
          EIAEGIM.RHRF.SAYE....PPD..WQYLLMAA..YETI.FKV.SREIDKAE.KFWTHWNRETKQFFLQ
Retrocopy EIAEGIMLRHRFTSAYEPQLQPPDWLWQYLLMAAKTYETITFKVLSREIDKAEDKFWTHWNRETKQFFLQ

Parental  FHFKMEKPPAPPSLPAGPPGVKRPPPPLMNGLPPRPPLPESLPPPPPGGLPLPPMPP-TGPAPSGPPGPP
          FHFKM.KPPAPP.LP.GPPGVKRPPPPLM..LPPRPPLPESLPPPPPGGLPLPPMPP...PAPSGPPGPP
Retrocopy FHFKMQKPPAPPTLPTGPPGVKRPPPPLMTSLPPRPPLPESLPPPPPGGLPLPPMPP>MRPAPSGPPGPP

Parental  QLPPPAPGVHPPAPVVHPPTSGVHPPAPGVHPPAPGVHPPAPVVHPPTSGVHPPAPVVHPPAPGVHPPAP
          QLPPPAP.VHP.APVVHP.TSGVHPPAPGVHPPAPGVHPPAPVVHPPTSGVHPPAP.VH.PAPGVHPPAP
Retrocopy QLPPPAPRVHPLAPVVHPATSGVHPPAPGVHPPAPGVHPPAPVVHPPTSGVHPPAPGVHTPAPGVHPPAP

Parental  GVHPPAPGVHPP
          GVHPPAPGVHPP
Retrocopy GVHPPAPGVHPP

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	1.66 RPM
SRP051959_heart	0.09 RPM	3.12 RPM
SRP051959_kidney	0.00 RPM	2.31 RPM
SRP051959_liver	0.00 RPM	2.10 RPM
SRP051959_lung	0.00 RPM	2.55 RPM
SRP051959_lymph_node	0.00 RPM	3.24 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.89 RPM
SRP051959_spleen	0.00 RPM	2.25 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3563 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3563 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3563 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013206	4 retrocopies	retro_cjac_1621, retro_cjac_2029, retro_cjac_3563 , retro_cjac_3971,
Otolemur garnettii	ENSOGAG00000033389	2 retrocopies	retro_ogar_3423, retro_ogar_3439,
Rattus norvegicus	ENSRNOG00000019349	1 retrocopy	retro_rnor_2822,