RetrogeneDB ID: | retro_btau_1069 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 25:3373124..3373631(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000026400 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BT.62733 | ||
| Ensembl ID: | ENSBTAG00000016312 | ||
| Aliases: | None | ||
| Description: | galectin-4 [Source:RefSeq peptide;Acc:NP_001029940] |
Retrocopy-Parental alignment summary:
>retro_btau_1069
ATGGCCTTTGTCCCTGCACCAGGCTACCAGCCCACCTACAACCCGACACTGCCCTACCACAACCCCATCCCAGGAGGTCT
CAGAGTTGGAATGTCCATTTACATGCAAGGAGTGGCTAGCGAGCACATGAAGAGGTTCTTCGTGAACTTCGAGGTGGGGC
AGGGCCAAGGGGCAGACGTCGCTTTCCACTTCAATCCCCGCTTTGATGGCTGGGATAAGGTGGTCTTGAACTCGAAGCAG
AATGGCTCGTGGGGCAACGAGGAGAGGAAAATGAGCATGCCCTTCCGCAAGGGTGCGGCCTTCGAGCTGGTGTTCATGGT
CATGATGGAGCACTTCAAGGTGGTGGTGAATGGGACTCCCTTCCATGAGTTTAAGCACCGGATCCCGCTGCAGATGGTCA
CCCACCTGCATGTGGATGGCGACCTGATGCTTCAATCAATTAACTTCATTGGAGGCCAGCCCCCCTCAAACCAGATGCCC
ATGCCTGCTAAGGCGTACCCAAGTCCC
ORF - retro_btau_1069 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.27 % |
| Parental protein coverage: | 50.9 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAFVPAPGYQPTYNPTLPYHNPIPGGLRVGMSVYIQGVASEHMKRFFVNFEVGQGQGADVAFHFNPRFDG |
| MAFVPAPGYQPTYNPTLPYHNPIPGGLRVGMS.Y.QGVASEHMKRFFVNFEVGQGQGADVAFHFNPRFDG | |
| Retrocopy | MAFVPAPGYQPTYNPTLPYHNPIPGGLRVGMSIYMQGVASEHMKRFFVNFEVGQGQGADVAFHFNPRFDG |
| Parental | WDKVVLNSKQNGSWGQEERKMSMPFRKGAAFELVFMVMTEHFKVVVNGTPFYEFKHRILLQMVTHLHVDG |
| WDKVVLNSKQNGSWG.EERKMSMPFRKGAAFELVFMVM.EHFKVVVNGTPF.EFKHRI.LQMVTHLHVDG | |
| Retrocopy | WDKVVLNSKQNGSWGNEERKMSMPFRKGAAFELVFMVMMEHFKVVVNGTPFHEFKHRIPLQMVTHLHVDG |
| Parental | DLMLQSINFIGGQPPSNQMPMPAQAYPMP |
| DLMLQSINFIGGQPPSNQMPMPA.AYP.P | |
| Retrocopy | DLMLQSINFIGGQPPSNQMPMPAKAYPSP |
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 .79 RPM | 23 .36 RPM |
| ERP005899_muscle | 20 .27 RPM | 892 .08 RPM |
| SRP017611_brain | 0 .14 RPM | 28 .28 RPM |
| SRP017611_kidney | 0 .06 RPM | 11 .62 RPM |
| SRP017611_liver | 0 .68 RPM | 39 .87 RPM |
| SRP030211_testis | 0 .16 RPM | 3 .46 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1069 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1069 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1069 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 | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000000156 | 1 retrocopy | |
| Bos taurus | ENSBTAG00000016312 | 1 retrocopy |
retro_btau_1069 ,
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