RetrogeneDB ID: | retro_cjac_1124 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 13:10077645..10078213(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PDLIM7 | ||
| Ensembl ID: | ENSCJAG00000006678 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1124
ATTGATTCCTTCAAAGCATTGCTGGAGGGGTCAGCACCTTGAGGCTTCTGGCTGCAAGGGGCAAGGACCTCAATGTACCC
TTCTCCATTTCCTGGCTCACTCCTGGAGGCAAATCAGTGCAGGCTGGTGTGGCTGTGGGTGACTGGGTGCTCATCAAAGG
TGAGAAGGCAGGAAGTTCACATATATCAAAGCCCAGAACAAGATCTGAGCCTGCATAAAGCGCCTCAGCCTGGGTCTCAG
CAGGTCTCAGCCAGTTCAGAGCAAACCACAGGAAGTCCTGGCTCCTGCCACAACCCCCCTGCAGTTCATACTTGCACCCA
GCACTTTCCTCAACAAGATGGCCTGGCCCTTTAGGGCACCCCTACCCGCTGGCAGTGCACCACAGAATGGACAGCTGCTC
CAACTGCTGGTCCCAGATGCCACCAAGCAGTGGTTGATGGAGAATACCAAGACTGGACACCATGGCCTGGGACAGGCCAG
TCGTGTTCCTTCAGCAAACTTGCCCACCTCATAGACACTAGTTCATGCAGACCTGGATGAGGAGCACCTGAAGAAATCAA
GGGAAAAG
ORF - retro_cjac_1124 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 69.19 % |
| Parental protein coverage: | 86.94 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | MDSFKVVLEGPAPWGFRLQG-GKDFNMPLSISRLTPGGKAAQAGVAVGDWVLSIDGENAGS-LTHIEAQN |
| .DSFK..LEG.AP.GF.LQG.GKD.N.P.SIS.LTPGGK..QAGVAVGDWVL.I.GE.AGS..T.I.AQN | |
| Retrocopy | IDSFKALLEGSAP*GFWLQG<GKDLNVPFSISWLTPGGKSVQAGVAVGDWVL-IKGEKAGS<FTYIKAQN |
| Parental | KIRACGERLSLGLSRAQPVQSKPQKAPAPAADPPRYTFAPSVSLNKTARPFGAPPPADNAPQQNGQPLRP |
| KI.AC..RLSLGLSR.QPVQSKPQ...APA..P.....APS..LNK.A.PF.AP.PA..AP.QNGQ.L.. | |
| Retrocopy | KI*ACIKRLSLGLSRSQPVQSKPQEVLAPATTPLQFILAPSTFLNKMAWPFRAPLPAGSAP-QNGQLLQL |
| Parental | LVPDASKQRLMENT-EDWRPRPGTGQSRSFRILAHLTGTE-FMQ-DPDEEHLKKSREK |
| LVPDA.KQ.LMENT..DW.P.PGTGQS.SF..LAHL..T..FMQ.D.DEEHLKKSREK | |
| Retrocopy | LVPDATKQWLMENT<QDWTPWPGTGQSCSFSKLAHLIDTS<FMQ<DLDEEHLKKSREK |
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 .00 RPM | 5 .90 RPM |
| SRP051959_heart | 0 .46 RPM | 17 .86 RPM |
| SRP051959_kidney | 0 .09 RPM | 2 .48 RPM |
| SRP051959_liver | 0 .11 RPM | 0 .89 RPM |
| SRP051959_lung | 0 .05 RPM | 4 .78 RPM |
| SRP051959_lymph_node | 0 .07 RPM | 3 .70 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 15 .09 RPM |
| SRP051959_spleen | 0 .00 RPM | 3 .38 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1124 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1124 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1124 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000006678 | 1 retrocopy |
retro_cjac_1124 ,
|
| Homo sapiens | ENSG00000196923 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000003146 | 1 retrocopy |