RetrogeneDB ID: retro_cjac_3825

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284794.1:30944..32282(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2R5E
• Ensembl ID: ENSCJAG00000019290
• Aliases: None
• Description: None

Sequence

>retro_cjac_3825
AAGCCCGTCAGAAAAGCCAGACAGAAGAGGTCGCAAAGTTCCTCACAGTTTAGGTCTCAAGGCAAGCCTGCTGAGTTAAC
ATCTCTGCCGCTGCTAAATGACGTTCCATCCTCAGAGCAGCCTGAGCTGTTTCTAAAGAAACTTCAGCAGTGCCGTGTCA
TTTTTGACTTCATGGACACGCTATCTGATCTTAAAATGAAAGAATGCAAGCACTCCACTCTTAACGAACTGGTGGGCTGT
ATTCCAATAAGCAGAGGCTGCTTGACAGAGCAGACTTACCCTGAAGTAGTTAGAATGGCATCTTGCAATATATTCAGAAC
TCTCCCTCCTAGTGACAGCCATGAATTTGATCCAGAAGAAGATGAGCCTACCCTTGAGGCATCGTGGCCACACTTACAGC
TTGTATATGAAGTTTTCATATGATTTTTGGAAAGCCAAGAATTCCAACCCAGCATTGCCAAAAACATATAGATCAGAAAT
GTGTATTACAGCTTCTGGAGCTATTTGACAGTGAAGACCCTTGGGAACGGAACTACTTAAAAACAGTTTTACACAGAATT
TCTGGCAAGTTTCTTGGTCTTAGAGCATTTATCTGAAAACAGATTAACAATATTTTTCCAAGGTTTGTTTATGAAACAGA
ACACTTCAATGGTATAGCTGAACTGCTGGAAATATTAGGAAGTATTCTCAATGGCTTTGCTTGACCTCTTAAGGCAGAAC
ACAAACAGTTTCTGGTGAAAGTGTTGATCCCCTTACACACTGTCAGGAGTTAATCTCTCTTCCATGCGCAGCTGGCATAT
TGTATAGTACAGTTTCTGGAGAAAGATCCTTCACTCACAGAACCAGTTATTAGGGGGTTAATGAAATTTTGGCCTGAAAC
ATGTAGTCAAAAAGAGGTCATATTCCTTGGGGAACTGGAAGAAATATTGGATGTGATTGAACGTTCACAATTTGTTAAAA
TCCAAGAACCTTTGTTTAAACAAATTGCCAAGTGTGTATCTAGCCCCCATTTTCAGGTGGCAGAAAGCGCACTCTATTAC
TGGAATGATGAATACATCATGAGTTTGATAGAAGAAAACTCTGACGTCATCCTTCCCATCATGTTTTCCAGCCTTTATAG
GGTTTCGAAAGTGGAGTGCAGCTATTGTGGCGTTAGAATACAACGTGTTGAAGGCATTTATGGAAATGAACAGCACCATG
TTTGACGAGCTGACAGCCACATACAAGTCAGATCGTCAGCGTGAGAAAAAGAAAGAAAAGGAGCGTGAAGAACTGTGGAA
AAAATTGGAGGATCTGAAGTTAAAGAGAGGGCTTAGACGTGATGGAATAATTCCAACT

Alignment

ORF - retro_cjac_3825 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.11 %
• Parental protein coverage: 95.93 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KSVRKARQKRSQSSSQFRSQGKPIELTPLPLLKDVPSSEQPELFLKKLQQCCVIFDFMDTLSDLKMKEYK
          K.VRKARQKRSQSSSQFRSQGKP.ELT.LPLL.DVPSSEQPELFLKKLQQC.VIFDFMDTLSDLKMKE.K
Retrocopy KPVRKARQKRSQSSSQFRSQGKPAELTSLPLLNDVPSSEQPELFLKKLQQCRVIFDFMDTLSDLKMKECK

Parental  RSTLNELVDYITISRGCLTEQTYPEVVRMVSCNIFRTLPPSDSNEFDPEEDEPTLEASWPHLQLVYEFFI
          .STLNELV..I.ISRGCLTEQTYPEVVRM.SCNIFRTLPPSDS.EFDPEEDEPTLEASWPHLQLVYE.FI
Retrocopy HSTLNELVGCIPISRGCLTEQTYPEVVRMASCNIFRTLPPSDSHEFDPEEDEPTLEASWPHLQLVYEVFI

Parental  RFLESQEFQPSIAK-KYIDQKFVLQLLELFDSEDPRERDYLKTVLHRIYGKFLGLRAFIRKQINNIFLRF
          .FLESQEFQPSIAK.K.IDQK.VLQLLELFDSEDP.ER.YLKTVLHRI.GKFLGLRAFI.KQINNIF.RF
Retrocopy *FLESQEFQPSIAK<KHIDQKCVLQLLELFDSEDPWERNYLKTVLHRISGKFLGLRAFI*KQINNIFPRF

Parental  VYETEHFNGVAELLEILGSIINGFALPLKAEHKQFLVKVLIPLHTVRSLSLFHAQLAYCIVQFLEKDPSL
          VYETEHFNG.AELLEILGSI.NGFA.PLKAEHKQFLVKVLIPLHTVRS.SLFHAQLAYCIVQFLEKDPSL
Retrocopy VYETEHFNGIAELLEILGSILNGFA*PLKAEHKQFLVKVLIPLHTVRS*SLFHAQLAYCIVQFLEKDPSL

Parental  TEPVIRGLMKFWPKTCSQKEVMFLGELEEILDVIEPSQFVKIQEPLFKQIAKCVSSPHFQVAERALYYWN
          TEPVIRGLMKFWP.TCSQKEV.FLGELEEILDVIE.SQFVKIQEPLFKQIAKCVSSPHFQVAE.ALYYWN
Retrocopy TEPVIRGLMKFWPETCSQKEVIFLGELEEILDVIERSQFVKIQEPLFKQIAKCVSSPHFQVAESALYYWN

Parental  NEYIMSLIEENSNVIL-PIMFSSLYRISKEHWNPAIVALVYNVLKAFMEMNNTMFDELTATYKSDRQREK
          .EYIMSLIEENS.VIL.P..F.......K..W..AIVAL.YNVLKAFMEMN.TMFDELTATYKSDRQREK
Retrocopy DEYIMSLIEENSDVIL>PSCFPAFIGFRK--WSAAIVALEYNVLKAFMEMNSTMFDELTATYKSDRQREK

Parental  KKEKEREELWKKLEDLELKRGLRRDGIIPT
          KKEKEREELWKKLEDL.LKRGLRRDGIIPT
Retrocopy KKEKEREELWKKLEDLKLKRGLRRDGIIPT

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	0.04 RPM	17.99 RPM
SRP051959_heart	0.14 RPM	15.66 RPM
SRP051959_kidney	0.04 RPM	14.07 RPM
SRP051959_liver	0.04 RPM	9.62 RPM
SRP051959_lung	0.08 RPM	15.97 RPM
SRP051959_lymph_node	0.07 RPM	19.50 RPM
SRP051959_skeletal_muscle	0.11 RPM	11.55 RPM
SRP051959_spleen	0.06 RPM	17.10 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3825 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3825 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3825 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002574	1 retrocopy	retro_cjac_2146,
Callithrix jacchus	ENSCJAG00000019290	1 retrocopy	retro_cjac_3825 ,