RetrogeneDB ID: | retro_mmus_3697 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:133093942..133094990(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000082905 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Lcp1 | ||
| Ensembl ID: | ENSMUSG00000021998 | ||
| Aliases: | Lcp1, AW536232, D14Ertd310e, LCP-1, Pls2, pp65 | ||
| Description: | lymphocyte cytosolic protein 1 [Source:MGI Symbol;Acc:MGI:104808] |
Retrocopy-Parental alignment summary:
>retro_mmus_3697
GCTGACTACCACCTAGAAAACATAGGCTGCACCAAAATCACCAACTTCAGCACCGACATCAAGAACTCTGAAGCTTATTA
CCACCTGCTCAAGCAAGTGGTTCCAAAGGGAGATGAAGAAGGGATCCCGGATGTTGTGATTGACAAGTCAGGACTGAGGG
AGAAGGATGACATCCAGAGGGCAGAGTGCATGCTGCAACAGGCGGAGAGACTAGGCTGCCAGCAGTTTGTCAGCTACCGA
CGTTGTCTGAGGGAATCCCAAGTTGAACCTGGCCTTCATTGCCAACCTCTTTAACAAATACCTTGCCTTACACAAACCAG
AGAACCAGGACATTGACTGGGGGGCTCTCGAAGGTGAGATGAGGGAAGAACGGACATACAGGAACTGGATGAACTCCCTG
GGAGTTAACCCTTGAGTCAATCATTTTTACAGCGACTTATCAGATGCCTTAGTCATCTTCCAGCTCTATGAAAAGATCAA
AGTCCCTGTTGACTGGAACAGAGTAAACAAGCCTCCATACCCCAATACGAAAAAGCTGGAGAACTGTAATTATGCAGTAG
ATCTGGGGAAGAATCAAGCTAAATTCTCCTTGGTTGGCATCGCAGGACAAGACCTCAATGAAGGAAACCACACTCTCACG
CTGGCATTGGTTTGGCAGCTCATGAAAAGGTACACACTGAATATCCTGGAAGATATCAGAAGTGGACAGAAGGTCAATGA
TTACATTATTGTCAACTGGGTAAATACAACCTTGAAGGAGGCACAGAAAAGCTTGTCCATTGCTAGCTTCAAGGACCTAA
AGATCAGTACCAGCCTCCTGGTTCTGGATCCCATTGATGCCATTCAGCCGGGTTCCATAAACTATGGCCTTCTAAAGACA
GAAAACCTGGATGATGAAGAGAAACTCAACAATGCAAAGTATGCCATCTCTATGGCCAGAAAAATCAGAGCAAGGGTGTA
CGAGCTCCCATAAGACCTGGCTGAAGTAAACCCCAAAATGGTCATGACCGTGTTTGCCTGCCTCATGGGGATAGGGATGA
AGACGGTG
ORF - retro_mmus_3697 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.64 % |
| Parental protein coverage: | 56.46 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | ANYHLENAGCTKITNFSTDIKDSKAYYHLLEQVAPKGDEEGIPAVVIDMSGLREKDDIQRAECMLQQAER |
| A.YHLEN.GCTKITNFSTDIK.S.AYYHLL.QV.PKGDEEGIP.VVID.SGLREKDDIQRAECMLQQAER | |
| Retrocopy | ADYHLENIGCTKITNFSTDIKNSEAYYHLLKQVVPKGDEEGIPDVVIDKSGLREKDDIQRAECMLQQAER |
| Parental | LGCRQFVTATDVVR-GNP-KLNLAFIANLFNKYPALHKPENQDIDWGALEGETREERTFRNWMNSLGVNP |
| LGC.QFV......R.G.P.KLNLAFIANLFNKY.ALHKPENQDIDWGALEGE.REERT.RNWMNSLGVNP | |
| Retrocopy | LGCQQFVSYRRCLR<GIP<KLNLAFIANLFNKYLALHKPENQDIDWGALEGEMREERTYRNWMNSLGVNP |
| Parental | RVNHLYSDLSDALVIFQLYEKIKVPVDWNRVNKPPYPKLGGNMKKLENCNYAVDLGKNQAKFSLVGIAGQ |
| .VNH.YSDLSDALVIFQLYEKIKVPVDWNRVNKPPYP....N.KKLENCNYAVDLGKNQAKFSLVGIAGQ | |
| Retrocopy | *VNHFYSDLSDALVIFQLYEKIKVPVDWNRVNKPPYP----NTKKLENCNYAVDLGKNQAKFSLVGIAGQ |
| Parental | DLNEGNRTLTLALVWQLMRRYTLNILEDIGGGQKVNDDIIVNWVNTTLKEAQKSSSIASFKDPKISTSLP |
| DLNEGN.TLTLALVWQLM.RYTLNILEDI..GQKVND.IIVNWVNTTLKEAQKS.SIASFKD.KISTSL. | |
| Retrocopy | DLNEGNHTLTLALVWQLMKRYTLNILEDIRSGQKVNDYIIVNWVNTTLKEAQKSLSIASFKDLKISTSLL |
| Parental | VLDLIDAIQPGSINYDLLKTENLDDEEKLNNAKYAISMARKIGARVYALPEDLVEVNPKMVMTVFACLMG |
| VLD.IDAIQPGSINY.LLKTENLDDEEKLNNAKYAISMARKI.ARVY.LP.DL.EVNPKMVMTVFACLMG | |
| Retrocopy | VLDPIDAIQPGSINYGLLKTENLDDEEKLNNAKYAISMARKIRARVYELP*DLAEVNPKMVMTVFACLMG |
| Parental | KGMKRV |
| .GMK.V | |
| Retrocopy | IGMKTV |
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 |
|---|---|---|
| SRP007412_brain | 0 .00 RPM | 7 .85 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 10 .64 RPM |
| SRP007412_heart | 0 .03 RPM | 26 .31 RPM |
| SRP007412_kidney | 0 .04 RPM | 49 .03 RPM |
| SRP007412_liver | 0 .00 RPM | 88 .45 RPM |
| SRP007412_testis | 0 .00 RPM | 2 .65 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3697 was not detected
No EST(s) were mapped for retro_mmus_3697 retrocopy.
No TSS is located nearby retro_mmus_3697 retrocopy 5' end.
retro_mmus_3697 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3697 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000012037 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000021998 | 2 retrocopies |
retro_mmus_1307, retro_mmus_3697 ,
|