RetrogeneDB ID: | retro_sscr_1201 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | X:71287801..71288871(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSSSCG00000030968 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RNFT1 | ||
| Ensembl ID: | ENSSSCG00000017671 | ||
| Aliases: | None | ||
| Description: | ring finger protein, transmembrane 1 [Source:HGNC Symbol;Acc:30206] |
Retrocopy-Parental alignment summary:
>retro_sscr_1201
CTGCCACTGTTCCTGTGGTGGCTGTCCGGGCCTCCATCCGCCCATCATCATGAGAGGAGACAGAGCCTTGAAGCCAAGAA
ATCTGAATCATAGAAAAAGTATTCAAGGGTAATGCAAGGCAACTGTAACCAACTGCACAGTTCTCCACAAACTGTAGGTG
GTGAGGATCCCTCAGTCTCCCAGTGTGTCCAAATGAGATTGACAGGAGAAGCCTCCTGTCTTTATTCTGGAGCTGTTCAT
ATCCAGATAAATGCATACCTAAAGAATGTGCTGAAAATCCAAGCTCCAGAAATGTAAGATCAGGTGTCCATGGCTGTACA
CATGGATGTATTCATAGTTGCTTACGGAGTCACTCCCACAATGAAGCAAGGCAGCCTGATGATACTTACACAGAGTCTGG
AGATCATGGTAGTAGCTCCTTCTCAGAATTCCAATATCTATTCAAGTGGCTTCAAAAAAGTCTTCCATATATTTTGATTC
TGGGTGTCAAACTTGTTATGCAGCATATTACAGGAATTTCTCTTGGAATTGGGCTGCTTACAACTTTTATATATGCAAAC
AAAAGCATTATAAATCAGGTTTTTCTAAGAGGAAGGTGCTTAAAGATCCAGTGTGCTTGGTTACTGGTATTCTCAGCAGG
ATCTTCTGTTCTTTTATATTATACCTTTCACTCTCAGTCACTTTATTACAGCTTAAGTTTTTTAAATCCCACTTTGGACT
ATTCGAGTTTCTGGGAAGTACTTTGAATTGTTGGAATTATAGACTTCATTCTGAAATTCCTCTTCATGGGCTTAAAATTC
TTTATTTTATTGGTGCCTTCTTTCATCATGCCTTTTAAATCCAAGGGTTATTGGTATATGCTTTTAGAAGAGTTATGTCA
GTATTACCGAACTTTTGTTTCCATACCAGTTTGGTTCCGTTACCTTATAAGCTATGGGGAGTTTGGTAATGTAACTAGAT
GGAATCTTAGAATATTTCTGGCTTTACTCTATCTCATAGTAAAACTTCTGGACTTTTTCGGACATCTGAAAACTTTCACA
TGGGTTTTGCGAATATTTTTTACACGACCA
ORF - retro_sscr_1201 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.66 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LPQFLRSLPGPWSAHRHERRQSLEAKNSESQKKYSRVMQANCSQLHSSPQTAGGEDASVSQCVQTRLTGE |
| LP.FL..L.GP.SAH.HERRQSLEAK.SES.KKYSRVMQ.NC.QLHSSPQT.GGED.SVSQCVQ.RLTGE | |
| Retrocopy | LPLFLWWLSGPPSAHHHERRQSLEAKKSES*KKYSRVMQGNCNQLHSSPQTVGGEDPSVSQCVQMRLTGE |
| Parental | ASCLYSGDVHIQINT-IPKECAENPSSRNVRSGVHSCTHGCVHSRLRSHSHNEARQPDDNDTESGDHGSS |
| ASCLYSG.VHIQIN..IPKECAENPSSRNVRSGVH.CTHGC.HS.LRSHSHNEARQPDD..TESGDHGSS | |
| Retrocopy | ASCLYSGAVHIQINA<IPKECAENPSSRNVRSGVHGCTHGCIHSCLRSHSHNEARQPDDTYTESGDHGSS |
| Parental | SFSEFRYLFKWLQKSLPYILILGVKLVMQHITGISLGIGLLTTFIYANKSIINQVFLRERCSKIQCAWLL |
| SFSEF.YLFKWLQKSLPYILILGVKLVMQHITGISLGIGLLTTFIYANKSIINQVFLR.RC.KIQCAWLL | |
| Retrocopy | SFSEFQYLFKWLQKSLPYILILGVKLVMQHITGISLGIGLLTTFIYANKSIINQVFLRGRCLKIQCAWLL |
| Parental | VFLAGSSVLLYYTFHSQSLYYSLIFLNPTLDYSSFWEVLWIVGITDFILKFLFMGLKCLILLVPSFVMPF |
| VF.AGSSVLLYYTFHSQSLYYSL.FLNPTLDYSSFWEVL.IVGI.DFILKFLFMGLK..ILLVPSF.MPF | |
| Retrocopy | VFSAGSSVLLYYTFHSQSLYYSLSFLNPTLDYSSFWEVL*IVGIIDFILKFLFMGLKFFILLVPSFIMPF |
| Parental | KSKGYWYMLLEELCQYYRTFVPIPVWFRYLISYGEFGNVTRWSLGILLALLYLILKLLDFFGHLKTFTRV |
| KSKGYWYMLLEELCQYYRTFV.IPVWFRYLISYGEFGNVTRW.L.I.LALLYLI.KLLDFFGHLKTFT.V | |
| Retrocopy | KSKGYWYMLLEELCQYYRTFVSIPVWFRYLISYGEFGNVTRWNLRIFLALLYLIVKLLDFFGHLKTFTWV |
| Parental | LRIFFTRP |
| LRIFFTRP | |
| Retrocopy | LRIFFTRP |
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 .40 RPM | 8 .63 RPM |
| SRP014902_testis | 0 .28 RPM | 15 .98 RPM |
| SRP018288_heart | 0 .60 RPM | 22 .53 RPM |
| SRP018288_kidney | 0 .69 RPM | 29 .95 RPM |
| SRP018288_liver | 0 .32 RPM | 27 .98 RPM |
| SRP018288_lung | 0 .20 RPM | 9 .67 RPM |
| SRP018856_adipose | 0 .00 RPM | 11 .27 RPM |
| SRP035408_brain | 0 .10 RPM | 0 .95 RPM |
| SRP035408_liver | 0 .68 RPM | 5 .87 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_1201 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_1201 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_1201 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000009747 | 2 retrocopies | |
| Cavia porcellus | ENSCPOG00000014736 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000017671 | 2 retrocopies |
retro_sscr_1201 , retro_sscr_523,
|