RetrogeneDB ID: retro_cjac_3848

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285052.1:11102..12242(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RANBP9
• Ensembl ID: ENSCJAG00000019797
• Aliases: None
• Description: RAN binding protein 9 [Source:HGNC Symbol;Acc:13727]

Sequence

>retro_cjac_3848
AAGGGAAGAGATGGTTACATGGGAATTGGTCTTTCTGCTCAAGGTGTGAACATGAATAGACTACCAGGTTGGGATAAGCA
TTCATATGGTTACCATGGGGATGATGGACATTCATTTTGTTCTTCTGGAACTGGACAACCTGATGGACCAGCTTTCACAA
CTGGTGATGTCATTGGCTGTTGTGTTAATCTTATCAACAATACCCGCTTTTACATCAAGAATGGACATAGTTTAGGTATT
GCTTTCACTGACCTACCGCCAAATTTGTATCCTACCATGGGGCTTCGGACACCAGGAGAAGTGGTTGATGCCAATTTTGG
TCAACATCCTTTCGTGTTTGATATAGAAGACTATATGTGAGAGTGGAGAACCAAAATCCAGGCACAGATAGACCGGTTTC
CTATCGGAGACCGAGAAGGAGAATGGCAGACCATGATACAAAAAATGGTTTCATCTTATTTAGTCCACCATGGGTACTGT
GCCACAGCAGAGGCCTTTGCCAGATCTACAGACCAGACCGGTCTAGAAGAATTGGCTTCCGTTAAGAATAGACAAAGAAT
TCAGAAATTGCTATTAGCAGGAAGAATGGGAGAAGCCATTGAAACAACACAACAGTTATACCCAAGTTTCCTTGAAAGAA
ATCCTAATCTCCTTTTCACATTAAAAGTACGTCCGTTTATAGAAATGGTGAATGGTACACATAGTGAAGTACGATGTTTG
GGAGGCCGAAGTCCAAAGACTCAAGACAGTTATCCTGTTAGTCCTCGACCTTTTAGTAGTCCAAGTATGATCCCCAGCCA
TGGAATGAATATCCACAATTTAGCATCAGGCAAAGGAAGGACTGCACATTTTTCTGGTTTTGAAAGTTGTAGTAATGGTG
TAATATCAAATAAAGCACATCAATCATATTGCCATAGTAATAAACACCAGTCATCCAATTTGAATGTACCAGAACTGAAC
AGTATAAATGCGTCAAAATCACAGCAAGTTAATAATTTCACCAGTAATGATGTAGACATGGAAACAGATCACTACTCCAA
CGGAGTTGGAGAAACTTCATCCAATGGTTTCCTAAATGGTAGCTCTAAACATGATCACGAAATGGAAGATTGTGACACCG
AAATGGAAGTTGATTCATCA

Alignment

ORF - retro_cjac_3848 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.01 %
• Parental protein coverage: 69.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KGRDGYMGIGLSAQGVNMNRLPGWDKHSYGYHGDDGHSFCSSGTGQPYGPTFTTGDVIGCCVNLINNTCF
          KGRDGYMGIGLSAQGVNMNRLPGWDKHSYGYHGDDGHSFCSSGTGQP.GP.FTTGDVIGCCVNLINNT.F
Retrocopy KGRDGYMGIGLSAQGVNMNRLPGWDKHSYGYHGDDGHSFCSSGTGQPDGPAFTTGDVIGCCVNLINNTRF

Parental  YTKNGHSLGIAFTDLPPNLYPTVGLQTPGEVVDANFGQHPFVFDIEDYMREWRTKIQAQIDRFPIGDREG
          Y.KNGHSLGIAFTDLPPNLYPT.GL.TPGEVVDANFGQHPFVFDIEDYM.EWRTKIQAQIDRFPIGDREG
Retrocopy YIKNGHSLGIAFTDLPPNLYPTMGLRTPGEVVDANFGQHPFVFDIEDYM*EWRTKIQAQIDRFPIGDREG

Parental  EWQTMIQKMVSSYLVHHGYCATAEAFARSTDQTVLEELASIKNRQRIQKLVLAGRMGEAIETTQQLYPSL
          EWQTMIQKMVSSYLVHHGYCATAEAFARSTDQT.LEELAS.KNRQRIQKL.LAGRMGEAIETTQQLYPS.
Retrocopy EWQTMIQKMVSSYLVHHGYCATAEAFARSTDQTGLEELASVKNRQRIQKLLLAGRMGEAIETTQQLYPSF

Parental  LERNPNLLFTLKVRQFIEMVNGTDSEVRCLGGRSPKSQDSYPVSPRPFSSPSMSPSHGMNIHNLASGKGS
          LERNPNLLFTLKVR.FIEMVNGT.SEVRCLGGRSPK.QDSYPVSPRPFSSPSM.PSHGMNIHNLASGKG.
Retrocopy LERNPNLLFTLKVRPFIEMVNGTHSEVRCLGGRSPKTQDSYPVSPRPFSSPSMIPSHGMNIHNLASGKGR

Parental  TAHFSGFESCSNGVISNKAHQSYCHSNKHQSSNLNVPELNSINMSRSQQVNNFTSNDVDMETDHYSNGVG
          TAHFSGFESCSNGVISNKAHQSYCHSNKHQSSNLNVPELNSIN.S.SQQVNNFTSNDVDMETDHYSNGVG
Retrocopy TAHFSGFESCSNGVISNKAHQSYCHSNKHQSSNLNVPELNSINASKSQQVNNFTSNDVDMETDHYSNGVG

Parental  ETSSNGFLNGSSKHDHEMEDYCDTEMEVDSS
          ETSSNGFLNGSSKHDHEMED.CDTEMEVDSS
Retrocopy ETSSNGFLNGSSKHDHEMED-CDTEMEVDSS

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	20.01 RPM
SRP051959_heart	0.00 RPM	22.64 RPM
SRP051959_kidney	0.00 RPM	19.75 RPM
SRP051959_liver	0.00 RPM	12.67 RPM
SRP051959_lung	0.03 RPM	24.40 RPM
SRP051959_lymph_node	0.07 RPM	28.88 RPM
SRP051959_skeletal_muscle	0.04 RPM	25.90 RPM
SRP051959_spleen	0.00 RPM	23.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3848 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3848 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3848 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006785	2 retrocopies	retro_chof_1695, retro_chof_512,
Callithrix jacchus	ENSCJAG00000016055	1 retrocopy	retro_cjac_3469,
Callithrix jacchus	ENSCJAG00000019797	1 retrocopy	retro_cjac_3848 ,