RetrogeneDB ID: retro_cjac_1621

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:2487989..2489191(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000007720
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_1621
ATGAACTTCCAGCATTGCCCTGGGGGCAAGACTGGGAGGGGGGCGTGGCCTCCTCCCAGAGCAACCGTGAGTGACCGCAG
GGAGCGCCTCCTGCAGCTGGCCCTGGAGACCATCGACATCAACAAGGACCCATATTTTATGAAAAACCACCTGGGCTCCT
ATGAATGCAATCTCTGCCTGACGTTTCACGACGAGGGGAGCTACCTGGCACACACCCAGGGGAAGAAGCACAAGACCAAC
TTGGCCCGGCGAGCGGCCAAGGATGCCAAGGAGGCCCCTGCCCAGCCTGCGCCTGAGAAGGTCAAGGTGGAGGTGAAGAA
GTTTGTGAAGATCGGCCACCCGGGCTACAAAGTGGCCAAGCAGAGGGACTCGGAGATGAGCCAGCAGAGCCTCCTCTTCC
AGATCGACTACCCTGAGATCGCGAGGGCATCATGCTGCGCCACCGCTTCACGTCTGCTTACGAGCTGCGGATCCAGCCCC
CGGACTGGCTCTGGCAGTACCTGCTGATGGCCGCCAAGCCCTACGAGACCATCGCCTTCAAGGTGCTGAGCAGAGAGATC
GACAAGGCGGAGGACAAGTTCTGGACCCACTGGAACCAGGAGACCAAGCAGTTCTTTCTCCAGTTCCACTTTAAGATGCG
GAAGACCCCGGCTCCGCCCAGCCTCCCGGCCGGACCCCCTGGAGAGAAGCGGCCTCCACCCCCGCTGATGACCGGTCTGC
CCCCTCGGCCACTGCTGCCCGAGTCTTTGCCACCGCCCCCGCCAGGAGGCCTGCTTCTGCCCTCCCATGCCCCCCGACGG
GGCCTGTGCCCTCAGGGCCCCCAGGACCACCCCAGCTGTCCCCACCAGCTCCACGGGTCCACCCACTGGCCCCAGTGGTG
CACCCCGCCACATCTGGAGTCCATCCCCCGGCTCCTGGGGTTCACCCCCCCAGCTCCTGGCGTCAATCCCCCAGCCCCTG
TGGTCCACCCACCAACCTCTGTGGTCCATCCCCCAGCTCCTGGAGTCCACCCTGCAGCCCCTGGGGTTCACCCACCAGCC
CCTGAGGTTCACCCACCAGCCCCTGGAGTCTACCCACCAGCCCCAGGGGTCCACCCTCCCCCATTAGCAGCAGTTCACCC
CCAGGTCCCAGGGTGGCACCCAGCAGCCCTGACCGTTCACCCTCAGGCCCTGGGGGTGCACCCACCAGCCCCAGGGATGC
AT

Alignment

ORF - retro_cjac_1621 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.77 %
• Parental protein coverage: 85.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MDFQHRPGGKTG-SGGVASSSESNR-DRRERLRQLALETIDINKDPYFMKNHLGSYECKLCLTLHNNEGS
          M.FQH.PGGKTG..GGVASS......DRRERL.QLALETIDINKDPYFMKNHLGSYEC.LCLT.H..EGS
Retrocopy MNFQHCPGGKTG<EGGVASSQSNRE>DRRERLLQLALETIDINKDPYFMKNHLGSYECNLCLTFHD-EGS

Parental  YLAHTQGKKHQTNLARRAAKEAKEAPAQPAPEKVKVEVKKFVKIGRPGYKVTKQRDSEMGQQSLLFQIDY
          YLAHTQGKKH.TNLARRAAK.AKEAPAQPAPEKVKVEVKKFVKIG.PGYKV.KQRDSEM.QQSLLFQIDY
Retrocopy YLAHTQGKKHKTNLARRAAKDAKEAPAQPAPEKVKVEVKKFVKIGHPGYKVAKQRDSEMSQQSLLFQIDY

Parental  PEIA-EGIMPRHRFMSAYEQRIEPPDRRWQYLLMAAEPYETIAFKVPSREIDKAEGKFWTHWNRETKQFF
          PEIA.EGIM.RHRF.SAYE.RI.PPD..WQYLLMAA.PYETIAFKV.SREIDKAE.KFWTHWN.ETKQFF
Retrocopy PEIA<EGIMLRHRFTSAYELRIQPPDWLWQYLLMAAKPYETIAFKVLSREIDKAEDKFWTHWNQETKQFF

Parental  LQFHFKMEKPPAPPSLPAGPPGVKRPPPPLMNGLPPRPPLPESLPPPPPGGLPL-PPM-PPTGPAPSGPP
          LQFHFKM.K.PAPPSLPAGPPG.KRPPPPLM.GLPPRP.LPESLPPPPPGGL.L.PPM.PPTGP.PSGPP
Retrocopy LQFHFKMRKTPAPPSLPAGPPGEKRPPPPLMTGLPPRPLLPESLPPPPPGGLLL>PPM>PPTGPVPSGPP

Parental  GPPQLPPPAPGVHPPAPVVHPPTSGVHPPAPGVH-PPAPGVHPPAPVVHPPTSGVHPPAPVVHPPAPGVH
          GPPQL.PPAP.VHP.APVVHP.TSGVHPPAPGVH.PPAPGV.PPAPVVHPPTS.VHPPAP.VHP.APGVH
Retrocopy GPPQLSPPAPRVHPLAPVVHPATSGVHPPAPGVH>PPAPGVNPPAPVVHPPTSVVHPPAPGVHPAAPGVH

Parental  PPAPGVHPPAPGVHPPAPGVHPPP-AAVHPQAPGVHPAAPAPAP---GVHPPAPGVH
          PPAP.VHPPAPGV.PPAPGVHPPP.AAVHPQ.PG.HPAA....P...GVHPPAPG.H
Retrocopy PPAPEVHPPAPGVYPPAPGVHPPPLAAVHPQVPGWHPAALTVHPQALGVHPPAPGMH

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	0.00 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_1621 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1621 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1621 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,