RetrogeneDB ID: retro_cjac_4161

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:46117724..46118959(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ITPK1
• Ensembl ID: ENSCJAG00000018249
• Aliases: None
• Description: None

Sequence

>retro_cjac_4161
ATGCAGACTTTTCGGAAAGGCAAGAGAGTTGGCTACTGGCTCAGTGGGAAGAAAACCAAGAAGCTCAATTTCCAAGCCTT
AGCAGAGCAGTGCAGGAAGTGAGGGATAGAAGTCGTACAGCTAAACCTTAGCCAGGTGGAGCAGGGACCCCTGGATGTCA
TAATTCACAAGTTGAACGTCATCCTTGAAGCTGACCAGAATGAAAGCCAGTACCTGGAGCTCGTGCAAAGGTTTCAGGAG
TACATCGATGCCCACCCTGAGACCATCATCCTGGATCCCTTCCCTGACATCAGAACCCTGCTCGACAACTCCAAGTCCTG
CAAGCTCATCTGGAAGATTGAGGTCTACATGGAAGATGACAGATCTGCTCACTGCCCTTCATGGGGCACGAGCCTGTGCG
GGGATGACACCACGTAGCTACTGGAGAACGGCCTGGCTTTCCCGTTCATTTGCAAAACCAGAGTGGCAACAGCACCAACT
CTCATGAGATGGCTACTGTGTTCAACCAGGAGGGCCTGAACGGCATCCAGCCACCCTGTGTGGTCCAGAATTTCATCAAC
CACAACACTGTTCTGTACAAGGTGTTCATGGTCAGTGAGTCCTACACCATGGTTCAGAGGCCTTGCTCAAGAACTTCTCC
ACAGGCACAATGTAACCACAAGTCCATCTTCTTCAATAGCTACAATGTGTCAAAGCCGGAGTCATCATCGGTCCTGACGG
GAGCTGGACAAAATCGAGGGATCTGGTCTGTTCAAGCACAGCCAAGCAATGAGGTCATCCAGGAGCTCTCCCGGGCCCTG
CAGCAAGTGCTGGGCATATGGCTGTTCAGCATGGACATCGTCATCAACAACCAGATGGGGCAGCATGCCGTCATTGACAT
GAATGCCTTCCCAGGATACGAGGGCATAAGCGAGTTTTTCACAGACTTCCACAACCACACCACCGAAGTCTTGCAAGTCC
AGAGCACAGCCATGGGAGCCACGGGGTATGTGGCCCCACTGAGGCACAGCAAGCTCCTGGCCAAGTCAGCGGGCAGCCTG
GCAGGCGAGCAGACATGCATCGCCAGCCCTGGCTGCTGCAGCAGCATGATAGGCCAGGACGCACCCTGGAAGACCGAGGC
CAATACAGGTGGTACCGCCAAAATGCCACACCAGAGACTCAGCTACACCACCCATGTGTTGCCCAGCTTCCAACAGCACT
GTGTGGCCTCCCTGGCCACTAAGGCCTCCTCCCAG

Alignment

ORF - retro_cjac_4161 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MQTFLKGKRVGYWLSEKKIKKLNFQAFAELCRKRGIEVVQLNLNRPIEEQGPLDVIIHKLTDVILEADQN
          MQTF.KGKRVGYWLS.KK.KKLNFQA.AE.CRK.GIEVVQLNL.....EQGPLDVIIHKL..VILEADQN
Retrocopy MQTFRKGKRVGYWLSGKKTKKLNFQALAEQCRK*GIEVVQLNLSQV--EQGPLDVIIHKL-NVILEADQN

Parental  DSQSLELVHRFQEYIDAHPETIILDPLPAIRTLLDRSKSYELIRKIEAYMEDDRICSPPFMELTSLCGDD
          .SQ.LELV.RFQEYIDAHPETIILDP.P.IRTLLD.SKS..LI.KIE.YMEDDR....P....TSLCGDD
Retrocopy ESQYLELVQRFQEYIDAHPETIILDPFPDIRTLLDNSKSCKLIWKIEVYMEDDRSAHCPSWG-TSLCGDD

Parental  TMRLLEKNGLAFPFICKTRVA-HGTNSHEMAIVFNQEGLNAIQPPCVVQNFINHNAVLYKVFVVGESYTV
          T..LLE.NGLAFPFICKTRVA...TNSHEMA.VFNQEGLN.IQPPCVVQNFINHN.VLYKVF.V.ESYT.
Retrocopy TT*LLE-NGLAFPFICKTRVA<NSTNSHEMATVFNQEGLNGIQPPCVVQNFINHNTVLYKVFMVSESYTM

Parental  VQRPS-LKNFSAGTS-DRESIFFNSHNVSKPESSSVLTELDKIEGVFE---RPSDEVIRELSRALRQALG
          VQRP..LKNFS.GT.....SIFFNS.NVSKPESSSVLT......G.......PS.EVI.ELSRAL.Q.LG
Retrocopy VQRPC<LKNFSTGTM>NHKSIFFNSYNVSKPESSSVLTGAGQNRGIWSVQAQPSNEVIQELSRALQQVLG

Parental  VSLFGIDIIINNQTGQHAVIDINAFPGYEGVSEFFTDLLNHIATVLQGQSTATAAAGDVAPLRHSKLLAE
          ..LF..DI.INNQ.GQHAVID.NAFPGYEG.SEFFTD..NH...VLQ.QSTA..A.G.VAPLRHSKLLA.
Retrocopy IWLFSMDIVINNQMGQHAVIDMNAFPGYEGISEFFTDFHNHTTEVLQVQSTAMGATGYVAPLRHSKLLAK

Parental  PAGGLAGERTCSASPGCCSSMMGQDTPWKAEADAGGTTKLPHQRLGCTTGVSPSFQQHCVASLATKASSQ
          .AG.LAGE.TC.ASPGCCSSM.GQD.PWK.EA..GGT.K.PHQRL..TT.V.PSFQQHCVASLATKASSQ
Retrocopy SAGSLAGEQTCIASPGCCSSMIGQDAPWKTEANTGGTAKMPHQRLSYTTHVLPSFQQHCVASLATKASSQ

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	0.87 RPM	18.17 RPM
SRP051959_heart	0.54 RPM	12.42 RPM
SRP051959_kidney	0.51 RPM	9.10 RPM
SRP051959_liver	0.43 RPM	5.96 RPM
SRP051959_lung	0.63 RPM	13.89 RPM
SRP051959_lymph_node	0.87 RPM	12.21 RPM
SRP051959_skeletal_muscle	0.37 RPM	6.49 RPM
SRP051959_spleen	0.84 RPM	14.87 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4161 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4161 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4161 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4823

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018249	1 retrocopy	retro_cjac_4161 ,
Homo sapiens	ENSG00000100605	1 retrocopy	retro_hsap_4823,
Nomascus leucogenys	ENSNLEG00000026648	1 retrocopy	retro_nleu_2198,