RetrogeneDB ID: retro_cjac_2905

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:81980901..81981839(+)
• Located in intron of: ENSCJAG00000021178

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIP4K2C
• Ensembl ID: ENSCJAG00000006988
• Aliases: None
• Description: phosphatidylinositol-5-phosphate 4-kinase, type II, gamma [Source:HGNC Symbol;Acc:23786]

Sequence

>retro_cjac_2905
TCTGTCCCACCGGCCACCGTACCGGCGGCGACAGTGGGCCCCGGCACAGGTTTCGGCTTCGCCTCCAAAACCAAGAAGAA
GCATTTCGTGCAGCAGAAGGTGAAGGTGTTGTGGGTGGCCCACCCACTGGTGGGTGTGTTCCTGTGGGGCGTAGCCCACT
GGATCAATGAGCTCAGCCAGGTGCCTCCCCAGGTGATGCTGCTGCCAGATGACTTTAAGGCCAGCTCCAAGATCAAGGTC
AACAATCACCTTTTCCACAGGGAAAATCTGCCCAGTCACTTCAAGTTCAAGGAGTATTGTCCCCAGGTCTTCAGGAATCT
CCGTGATCGATTTGGCAGTGATGACCAAGGTTACCTGGTGTCCCTTACCCGAAACCCCCCCGCAAAAGTGAAGGCAATGA
TGGTCGCTTCCTAATTTCCTACAATCAGACTCTGGTCATCAAAGAAGTATCCAGTGAAGACATTGCTGACATGCATAGCA
ACCTCTCCAACTATCACCAGTACATTGTGAAGTGCCATGGCAACACACTTCTGCCCCAGTTCCTGGGGATGTACCGAGTC
AGTGTGGACAATGAAGACAGCTAAGTGCTTGTGATGCGCAATATGTTTAGCCACCGTCTTCCAGTGCACAGGAAGTATGA
CCTCAAGGGTTCCCTAGTGTCCCGGGAAGCCAGCGACAAGGAAAAGGTTAAAGAATTGCCCACGCTTAAGGATATTGACT
TTCTCAGCAAGAACCAGAAAGTATATATTGGTGAAGAGGAGAAGAAAATATTTCTGGAGAAGCTAAAGAGAGATGTGGAG
TTTCTAGTGCAGCTGAAGATCATGGACTACAGCCTTCTGCTGGGCATCCAGGACATCATTCGGGGCTCTGCACCAGAGGA
GGATGAGTCAGAGGTGGATGGGGACTGCAGTCTCACTGGACCTCCTGCTCTGGTGGGC

Alignment

ORF - retro_cjac_2905 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.22 %
• Parental protein coverage: 74.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVPPATVPAATAGPGTGFGFASKTKKKHFVQQKVKVFRAADPLVGVFLWGVAHSINELSQVPPPVMLLPD
          SVPPATVPAAT.GPGTGFGFASKTKKKHFVQQKVKV...A.PLVGVFLWGVAH.INELSQVPP.VMLLPD
Retrocopy SVPPATVPAATVGPGTGFGFASKTKKKHFVQQKVKVLWVAHPLVGVFLWGVAHWINELSQVPPQVMLLPD

Parental  DFKASSKIKVNNHLFHRENLPSHFKFKEYCPQVFRNLRDRFGIDDQCPQVSLTRNPPSK-SEGSDGRFLI
          DFKASSKIKVNNHLFHRENLPSHFKFKEYCPQVFRNLRDRFG.DDQ...VSLTRNPP.K.SEG.DGRFLI
Retrocopy DFKASSKIKVNNHLFHRENLPSHFKFKEYCPQVFRNLRDRFGSDDQGYLVSLTRNPPAK<SEGNDGRFLI

Parental  SYDRTLVIKEVSSEDIADMHSNLSNYHQYIVKCHGNTLLPQFLGMYRVSVDNEDSYMLVMRNMFSHRLPV
          SY..TLVIKEVSSEDIADMHSNLSNYHQYIVKCHGNTLLPQFLGMYRVSVDNEDS..LVMRNMFSHRLPV
Retrocopy SYNQTLVIKEVSSEDIADMHSNLSNYHQYIVKCHGNTLLPQFLGMYRVSVDNEDS*VLVMRNMFSHRLPV

Parental  HRKYDLKGSLVSREASDKEKVKELPTLKDMDFLSKNQKVYIGEEEKKIFLEKLKRDVEFLVQLKIMDYSL
          HRKYDLKGSLVSREASDKEKVKELPTLKD.DFLSKNQKVYIGEEEKKIFLEKLKRDVEFLVQLKIMDYSL
Retrocopy HRKYDLKGSLVSREASDKEKVKELPTLKDIDFLSKNQKVYIGEEEKKIFLEKLKRDVEFLVQLKIMDYSL

Parental  LLGIHDIIRGSEPEEEGPAREDESEVDGDCSLTG
          LLGI.DIIRGS.PEE............G...L.G
Retrocopy LLGIQDIIRGSAPEEDESEVDGDCSLTGPPALVG

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	2.24 RPM	15.29 RPM
SRP051959_heart	0.96 RPM	5.86 RPM
SRP051959_kidney	1.71 RPM	12.89 RPM
SRP051959_liver	1.45 RPM	7.43 RPM
SRP051959_lung	2.11 RPM	12.66 RPM
SRP051959_lymph_node	2.65 RPM	17.60 RPM
SRP051959_skeletal_muscle	0.87 RPM	4.37 RPM
SRP051959_spleen	1.70 RPM	11.53 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2905 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2905 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2905 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006988	1 retrocopy	retro_cjac_2905 ,