RetrogeneDB ID: | retro_sscr_1006 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 8:100272053..100272682(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CLAUDIN1 | ||
| Ensembl ID: | ENSSSCG00000028484 | ||
| Aliases: | None | ||
| Description: | Sus scrofa claudin 1 (CLDN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001244539] |
Retrocopy-Parental alignment summary:
>retro_sscr_1006
GCCAACGCGGGGCTGCAGCTGCTGGGCTTCATCCTGGCCTTCCTGGGCTGGATCGGCTCCATCGTCAGCACCGCACTGCT
TCAGTGTAAGATTTACTCCTACGCTGGTGACAACATAGTGACAGTCCAGGCCATCTAGGAGGGGCTGTGGATGTCCCGCA
TGTCGCAGAGCACCGGGAAGATCCAGTGCAAAGTCTTAGACTCCTTGCTGAATCTGAACAGCACTATGCAAGCAACCCGT
GCCTTGATAGTGACTGGCATCCTTCTGGGACTATACCCATCTTTGTGGCCACCATTGGCATGAAGTGTATGAAGTGCATG
GAAGATGATGAGGTGCAGAAGATGTGGATGGCTGTCATTGGGGGAGTGATCTTTCTTATTTCAGGTCTGGCTATCTTAGT
TGCCACAGCATAGTATGGTAACAGAATTGTTCAAGAATTCTATCACCTCATGACCCCGGTCAATGCCAGATATGAATTTG
GTCAGGCTCTCTTCACTGGCTGGGCTGCTGCTTCTCTCTGCCTTCTGGGAGGTGCCCTACTTTGCCGCTCCTGTCCCCGA
AAAACAACATCTTACCCAACACAAAGGCCCTATCCAAAACCTTCACCTTCCAGTGGGAAAGACTACGTG
ORF - retro_sscr_1006 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.94 % |
| Parental protein coverage: | 99.53 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | ANAGLQLLGFILAFLGWIGSIVSTALPQWKIYSYAGDNIVTAQAIYEGLWMSCVSQSTGQIQCKVFDSLL |
| ANAGLQLLGFILAFLGWIGSIVSTAL.Q.KIYSYAGDNIVT.QAI.EGLWMS..SQSTG.IQCKV.DSLL | |
| Retrocopy | ANAGLQLLGFILAFLGWIGSIVSTALLQCKIYSYAGDNIVTVQAI*EGLWMSRMSQSTGKIQCKVLDSLL |
| Parental | NLNSTLQATRALMVIGILLGL-IAIFVATVGMKCMKCMEDDEVQKMRMAVIGGVIFLISGLAILVATAWY |
| NLNST.QATRAL.V.GILLGL.I.IFVAT..................MAVIGGVIFLISGLAILVATA.Y | |
| Retrocopy | NLNSTMQATRALIVTGILLGL<IPIFVATIXXXXXXXXXXXXXXXXWMAVIGGVIFLISGLAILVATA*Y |
| Parental | GNRIVQEFYDPMTPVNARYEFGQALFTGWAAASLCLLGGALLCCSCPRKTTSYPTPRPYPKPSPSSGKDY |
| GNRIVQEFY..MTPVNARYEFGQALFTGWAAASLCLLGGALLC.SCPRKTTSYPT.RPYPKPSPSSGKDY | |
| Retrocopy | GNRIVQEFYHLMTPVNARYEFGQALFTGWAAASLCLLGGALLCRSCPRKTTSYPTQRPYPKPSPSSGKDY |
| Parental | V |
| V | |
| Retrocopy | V |
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 | 122 .78 RPM |
| SRP014902_testis | 0 .00 RPM | 0 .14 RPM |
| SRP018288_heart | 0 .00 RPM | 0 .34 RPM |
| SRP018288_kidney | 0 .00 RPM | 8 .18 RPM |
| SRP018288_liver | 0 .32 RPM | 57 .09 RPM |
| SRP018288_lung | 0 .00 RPM | 3 .46 RPM |
| SRP018856_adipose | 0 .02 RPM | 1 .41 RPM |
| SRP035408_brain | 0 .00 RPM | 0 .19 RPM |
| SRP035408_liver | 0 .00 RPM | 14 .50 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_1006 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_1006 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_1006 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 | |
|---|---|---|---|
| Equus caballus | ENSECAG00000021074 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000028484 | 1 retrocopy |
retro_sscr_1006 ,
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