RetrogeneDB ID: | retro_sscr_459 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 15:69163690..69164368(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LCLAT1 | ||
| Ensembl ID: | ENSSSCG00000025901 | ||
| Aliases: | None | ||
| Description: | Sus scrofa lysocardiolipin acyltransferase 1 (LCLAT1), mRNA. [Source:RefSeq mRNA;Acc:NM_001142845] |
Retrocopy-Parental alignment summary:
>retro_sscr_459
GACTATTTTTGCGATTTCCATGAACCACTTCAACTCCTCATATTCCTAGAAGGAACTGATTTCACAGAAAACAGCGTAGT
TCAAAATAATGAATTTGCTGAAAAGAATGGACTTCTGAAATATGCCTATGTCTTACATTCAAGAACCACAGGCTTTACTT
TGGTAGCAGACTGTGTAAGAGAAGGTAAAAATCTGCATGCTGGCCGTGACTTCATGGTGACAAACCCTCACAACACACCT
CAGACAGAGAGACACCTTCTCCTTGGGGGCTTTCCCAAAGAGATCCACTTCCATGTCCACTGACACCGGTGGACACCCTC
CCCTTGTCCAGAGAGGACCTCCAGCTCTGGTGCCACAAACAATGGTAAGAGAAAGAAAGAGGCTGTGCCCCTTCTATTGA
GGGGAGAAGAATTTTTACTTTAGGGGACAGACTATCATTCTACTTGTAAATCTAAGCCCAGAGTCCTTGTTTGAGGTCAA
ATTGCTTTCTACTGGACCCTGTTCAGCCCTGCAATGTGCCTGTTCATCTGTTTATACAGTATTGTTTGGTGGTATTTTAT
AATCATCACTGTCATTTTTGTGCTGCAGGAGAGAATATTTGGTGGACTAGAGATCATCAAACTTGCATGTAAACTTTTTT
TTTTTTAATACAAACAGTCACATTTAAATGCAAAGAAA
ORF - retro_sscr_459 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.83 % |
| Parental protein coverage: | 60.11 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | DYFCNIHEPLQLLIFPEGTDLTENSTARSNEFAEKNGLQKYEYVLHPRTTGFTFVVDRLREGKNLDAVHD |
| DYFC..HEPLQLLIF.EGTD.TENS....NEFAEKNGL.KY.YVLH.RTTGFT.V.D..REGKNL.A..D | |
| Retrocopy | DYFCDFHEPLQLLIFLEGTDFTENSVVQNNEFAEKNGLLKYAYVLHSRTTGFTLVADCVREGKNLHAGRD |
| Parental | ITVAYPHNIPQTERHLLLGDFPKEIHFHVHRY-PVASLPASKEDLQLWCHKRWEEKE-ARLRSFYRGEKN |
| ..V..PHN.PQTERHLLLG.FPKEIHFHVH...PV..LP.S.EDLQLWCHK.W.EKE..RL..FY.GEKN | |
| Retrocopy | FMVTNPHNTPQTERHLLLGGFPKEIHFHVH*H<PVDTLPLSREDLQLWCHKQW*EKE<KRLCPFY*GEKN |
| Parental | FAFTGQTVI-PPCKSELRVLVVKWLSILYWTLFSPAMCLLIYFYSLARWYFIIIIVILVLQERLFGGLEL |
| F.F.GQT.I...CKS..RVLV.......YWTLFSPAMCL.I..YS...WYFIII.VI.VLQER.FGGLE. | |
| Retrocopy | FYFRGQTII<STCKSKPRVLV*GQIA-FYWTLFSPAMCLFICLYSIVWWYFIIITVIFVLQERIFGGLEI |
| Parental | IELAC--YRFLHKQPHLNAKK |
| I.LAC.......KQ.HLNAKK | |
| Retrocopy | IKLACKXXXXXYKQSHLNAKK |
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 |
|---|---|---|
| SRP014902_placenta | 0 .00 RPM | 5 .04 RPM |
| SRP014902_testis | 0 .00 RPM | 4 .24 RPM |
| SRP018288_heart | 0 .00 RPM | 9 .19 RPM |
| SRP018288_kidney | 0 .00 RPM | 4 .14 RPM |
| SRP018288_liver | 0 .00 RPM | 6 .72 RPM |
| SRP018288_lung | 0 .00 RPM | 5 .09 RPM |
| SRP018856_adipose | 0 .00 RPM | 0 .60 RPM |
| SRP035408_brain | 0 .00 RPM | 0 .38 RPM |
| SRP035408_liver | 0 .00 RPM | 1 .47 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_459 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_459 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_459 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Sus scrofa | ENSSSCG00000025901 | 1 retrocopy |
retro_sscr_459 ,
|
| Tursiops truncatus | ENSTTRG00000013682 | 1 retrocopy |