RetrogeneDB ID: retro_cjac_2029

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:29858853..29859707(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000013852
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_2029
ACCCGGAGCACCCGTGACCGCAGCGAGCGCGTCCGGCAGCTGGCCCTGGAGACCATCGACATCGACAAGGACCCGTACTT
CATGAAAAACCACCTGGGCTCCTATGAATGCAGCTCTGCCTGACGCTTCACAACAACGAGGGGAGCTACCTGGCACAAAC
CCAGGGGAAGAAGCACCAGACCAACCTGGCCCGTCTAGCGGCCAAGGAGGCCAAGGAGGCCCCCACCCAGCCTGCGCCTG
AGAAGGTCAAGGTGGAGGTGAAGAAGTTTGTGAAGATCGGCCGCCCGGGCTACAAAGTGACCAAGCAGAGGGACTCGGAG
ATGGGCCAGCAGAGCCTCCTCTTGCAGATCGACTACCCTGAGATCGCCGAGGGCATCATGCCGGGCCACCGCTTCATGTC
TGCCTGCGAGCAGCGGATCGAGCCCCTGGACCAGCGCTGGCAGTACCTGCTGATGGCCGCCGAGCCCTATGAGACCATCG
CCTTCAAGGTGCCCAGAGAGATCGACAAGGCGGAGGGCAAGTTCTGGATGCATTGAACCGGGAGACCAAGCAATTCTTTC
TCCAGTTCCACTTTAAGATGGAGAAGCCCCCAGCCTCGCCCAGCCTCCCGGCCGGGCCCCCTGGGGTGAAGCAGCCTCCA
CCCCCACTGATCAACGGTCTGCCCCCTCGGCCACCGCGGCCTGAGTCTTTGCTGCCGCCCCTGCCAGGAGGCTGCCTCTG
CCACCCATGCCCCCCACGGGGCCTGCGTCCTCAGGGCCCCCAGGACCACCCCAGCTGTCCCTGCCAGCTCTAGGGGTCTA
CCCCCCGGCCCCAGTGGTGCAACCCCCAACATCTGGGGTCCACCCCCAGCTCCA

Alignment

ORF - retro_cjac_2029 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.57 %
• Parental protein coverage: 61.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SESNRDRRERLRQLALETIDINKDPYFMKNHLGSYEC-KLCLTLHNNEGSYLAHTQGKKHQTNLARRAAK
          ..S.RDR.ER.RQLALETIDI.KDPYFMKNHLGSYEC..LCLTLHNNEGSYLA.TQGKKHQTNLAR....
Retrocopy TRSTRDRSERVRQLALETIDIDKDPYFMKNHLGSYEC<QLCLTLHNNEGSYLAQTQGKKHQTNLARLXXX

Parental  EAKEAPAQPAPEKVKVEVKKFVKIGRPGYKVTKQRDSEMGQQSLLFQIDYPEIAEGIMPRHRFMSAYEQR
          .....P.QPAPEKVKVEVKKFVKIGRPGYKVTKQRDSEMGQQSLL.QIDYPEIAEGIMP.HRFMSA.EQR
Retrocopy XXXXXPTQPAPEKVKVEVKKFVKIGRPGYKVTKQRDSEMGQQSLLLQIDYPEIAEGIMPGHRFMSACEQR

Parental  IEPPDRRWQYLLMAAEPYETIAFKVPSREIDKAEGKFWTH-WNRETKQFFLQFHFKMEKPPAPPSLPAGP
          IEP.D.RWQYLLMAAEPYETIAFKVP.REIDKAEGKFW.H..NRETKQFFLQFHFKMEKPPA.PSLPAGP
Retrocopy IEPLDQRWQYLLMAAEPYETIAFKVP-REIDKAEGKFWMH<LNRETKQFFLQFHFKMEKPPASPSLPAGP

Parental  PGVKRPPPPLMNGLPPRPPLPESLPPPPPGG-LPLPPMPPTGPAPSGPPGPPQLPPPAPGVHPPAPVVHP
          PGVK.PPPPL.NGLPPRPP.PESL.PP.PGG.LPLPPMPPTGPA.SGPPGPPQL..PA.GV.PPAPVV.P
Retrocopy PGVKQPPPPLINGLPPRPPRPESLLPPLPGG<LPLPPMPPTGPASSGPPGPPQLSLPALGVYPPAPVVQP

Parental  PTSGVH-PPAP
          PTSGVH.PPAP
Retrocopy PTSGVH<PPAP

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	0.02 RPM	1.66 RPM
SRP051959_heart	0.00 RPM	3.12 RPM
SRP051959_kidney	0.02 RPM	2.31 RPM
SRP051959_liver	0.00 RPM	2.10 RPM
SRP051959_lung	0.08 RPM	2.55 RPM
SRP051959_lymph_node	0.00 RPM	3.24 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.89 RPM
SRP051959_spleen	0.02 RPM	2.25 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2029 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2029 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2029 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,