RetrogeneDB ID: | retro_btau_1690 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 9:410433..411234(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CASQ1 | ||
| Ensembl ID: | ENSBTAG00000020223 | ||
| Aliases: | None | ||
| Description: | calsequestrin-1 precursor [Source:RefSeq peptide;Acc:NP_001071345] |
Retrocopy-Parental alignment summary:
>retro_btau_1690
GGACTGACTGAAGAGGACAGAATTTATGTTTTCAAGGGGGATGAAGTCATTGAGTATGATGGTGAGTTTTCTGCTGACAC
CCTGGTGGAGTCTCTGCTTGATGTCCTGGAGGACCCTGTGGAATTGATTGAGGGTGAATGAAAGCTGCAGGCATTTGAGA
ATATTGAAGATGATAACAAACTCATTGGCTACTTCAAGAACAAGGACTCAGAGCATTACAAAGCCTACGAGGATGCAGTG
GAGGAGTTCCATCCCTACATCCCCTTCTTCACCACCTTCGACAGCAAGGTGGCAAAGAAGCTGACCCTAAAGCTAAATGA
AATTGACTTCTACAAGGCCTTCATGGAAGAGCCTGTGACCATCCCAGATAAGCCCAACAGTGAAGAGGAGATCATCAACT
TCGTGGAGGCACACAAAAGATCAACCCTGAGGAAGCTGAAGCCTGAGAGTATGTACGAGACTTGGGAGGAAGATGTGGAT
GGAATCCATATTGTGGCCTTTGCAGAGGAAGCTGATACTGATGGCTATGAGTTCTTAGAGACACTCAAGGCCGTGGCCCA
AGATAACACGGACAATCCTGACCTAAGCATCATCTGGATTGACCCTGATGACTTCCCCCTGCTGGTTCCATACTGGGAGA
AGACATTTAACATTGACTTGTCAGCCCCATAAATAGGAGTCATCAGTGTTACTGACGCGGACAGCATATAGATGGAAATG
GATGATGAGGAGGACCTGCCCTCTGCTGAGAAGCTGGAGGAATGGCTGGAGGATGTGCTGGAGGGTGAGATCAACACAGA
G
ORF - retro_btau_1690 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.13 % |
| Parental protein coverage: | 67.59 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | GLTEEDSVYVFKGDEVIEYDGEFSADTLVEFLLDVLEDPVELIEGERELQAFENIEDDNKLIGYFKNKDS |
| GLTEED..YVFKGDEVIEYDGEFSADTLVE.LLDVLEDPVELIEGE..LQAFENIEDDNKLIGYFKNKDS | |
| Retrocopy | GLTEEDRIYVFKGDEVIEYDGEFSADTLVESLLDVLEDPVELIEGE*KLQAFENIEDDNKLIGYFKNKDS |
| Parental | EHYKAYEDAAEEFHPYIPFFATFDSKVAKKLTLKLNEIDFYEAFMEEPVTIPDKPNSEEEIVSFVEAHKR |
| EHYKAYEDA.EEFHPYIPFF.TFDSKVAKKLTLKLNEIDFY.AFMEEPVTIPDKPNSEEEI..FVEAHKR | |
| Retrocopy | EHYKAYEDAVEEFHPYIPFFTTFDSKVAKKLTLKLNEIDFYKAFMEEPVTIPDKPNSEEEIINFVEAHKR |
| Parental | STLRKLKPESMYETWEDDLDGIHIVAFAEETDPDGYEFLETLKAVAQDNTDNPDLSIIWIDPDDFPLLVP |
| STLRKLKPESMYETWE.D.DGIHIVAFAEE.D.DGYEFLETLKAVAQDNTDNPDLSIIWIDPDDFPLLVP | |
| Retrocopy | STLRKLKPESMYETWEEDVDGIHIVAFAEEADTDGYEFLETLKAVAQDNTDNPDLSIIWIDPDDFPLLVP |
| Parental | YWEKTFNIDLSAPQIGVVNVTDADSVWMEMDDEEDLPSAEELEDWLEDVLEGEINTE |
| YWEKTFNIDLSAP.IGV..VTDADS..MEMDDEEDLPSAE.LE.WLEDVLEGEINTE | |
| Retrocopy | YWEKTFNIDLSAP*IGVISVTDADSI*MEMDDEEDLPSAEKLEEWLEDVLEGEINTE |
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 |
|---|---|---|
| ERP005899_liver | 0 .00 RPM | 0 .36 RPM |
| ERP005899_muscle | 0 .00 RPM | 0 .63 RPM |
| SRP017611_brain | 0 .00 RPM | 0 .96 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .53 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .08 RPM |
| SRP030211_testis | 0 .04 RPM | 4 .13 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1690 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1690 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1690 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000020223 | 1 retrocopy |
retro_btau_1690 ,
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