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 summary: | ||
| Parental gene symbol: | ITPK1 | ||
| Ensembl ID: | ENSCJAG00000018249 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_4161
ATGCAGACTTTTCGGAAAGGCAAGAGAGTTGGCTACTGGCTCAGTGGGAAGAAAACCAAGAAGCTCAATTTCCAAGCCTT
AGCAGAGCAGTGCAGGAAGTGAGGGATAGAAGTCGTACAGCTAAACCTTAGCCAGGTGGAGCAGGGACCCCTGGATGTCA
TAATTCACAAGTTGAACGTCATCCTTGAAGCTGACCAGAATGAAAGCCAGTACCTGGAGCTCGTGCAAAGGTTTCAGGAG
TACATCGATGCCCACCCTGAGACCATCATCCTGGATCCCTTCCCTGACATCAGAACCCTGCTCGACAACTCCAAGTCCTG
CAAGCTCATCTGGAAGATTGAGGTCTACATGGAAGATGACAGATCTGCTCACTGCCCTTCATGGGGCACGAGCCTGTGCG
GGGATGACACCACGTAGCTACTGGAGAACGGCCTGGCTTTCCCGTTCATTTGCAAAACCAGAGTGGCAACAGCACCAACT
CTCATGAGATGGCTACTGTGTTCAACCAGGAGGGCCTGAACGGCATCCAGCCACCCTGTGTGGTCCAGAATTTCATCAAC
CACAACACTGTTCTGTACAAGGTGTTCATGGTCAGTGAGTCCTACACCATGGTTCAGAGGCCTTGCTCAAGAACTTCTCC
ACAGGCACAATGTAACCACAAGTCCATCTTCTTCAATAGCTACAATGTGTCAAAGCCGGAGTCATCATCGGTCCTGACGG
GAGCTGGACAAAATCGAGGGATCTGGTCTGTTCAAGCACAGCCAAGCAATGAGGTCATCCAGGAGCTCTCCCGGGCCCTG
CAGCAAGTGCTGGGCATATGGCTGTTCAGCATGGACATCGTCATCAACAACCAGATGGGGCAGCATGCCGTCATTGACAT
GAATGCCTTCCCAGGATACGAGGGCATAAGCGAGTTTTTCACAGACTTCCACAACCACACCACCGAAGTCTTGCAAGTCC
AGAGCACAGCCATGGGAGCCACGGGGTATGTGGCCCCACTGAGGCACAGCAAGCTCCTGGCCAAGTCAGCGGGCAGCCTG
GCAGGCGAGCAGACATGCATCGCCAGCCCTGGCTGCTGCAGCAGCATGATAGGCCAGGACGCACCCTGGAAGACCGAGGC
CAATACAGGTGGTACCGCCAAAATGCCACACCAGAGACTCAGCTACACCACCCATGTGTTGCCCAGCTTCCAACAGCACT
GTGTGGCCTCCCTGGCCACTAAGGCCTCCTCCCAG
ORF - retro_cjac_4161 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.48 % |
| Parental protein coverage: | 100.0 % |
| 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 |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
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 |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4161 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4161 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4161 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_4823 |
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 | |
| Nomascus leucogenys | ENSNLEG00000026648 | 1 retrocopy |