RetrogeneDB ID: | retro_btau_1541 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 7:68122643..68123270(+) | ||
| Located in intron of: | ENSBTAG00000019457 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MGC159500 | ||
| Ensembl ID: | ENSBTAG00000021620 | ||
| Aliases: | PITHD1, C2H1orf128 | ||
| Description: | PITH domain-containing protein 1 [Source:RefSeq peptide;Acc:NP_001092360] |
Retrocopy-Parental alignment summary:
>retro_btau_1541
CTTTCGCATGGCCATAGTGGGGACGGCTGCTGCTGCGCCGCCAAACGGGAGGAGCCTCCCTAGCAGCGCGGCCTGACCTT
CGGCCTGTACCTGCTCTTTGACCTGGAGCAGTCTCAGTGCCTCAAGGAGAGCCATGAGGGCAGCGGCCCTGGCGTCTTTA
GGCCATGGGAGGAGCTGACTGACCGCTCCAAGTTTGTTGAAAGTGATGCAGATGAAGAGCTTATGTTAAATATTCCATGT
ACTGGCAATGTCAAGCTCAAGGGCATCATTATAATGGGAGACAATGATGACTCACACCCCTCTGAGATGAGACTGTACAG
GAACATTCCACAGATGTCCTTTGATGATAGAGACAAGGAGCCAGATCAGACCTTTAGTCTGAACTGGGATCTTACAGGGG
AATTAGAGTATGCTACAGAAATTTCTCATTTTTCAAATATCTGTCATCTCTCAATTCATATTTCAAAAAAATTTGGAGCT
GATACCACAAAGGTCTTTTATATTGGCCTGAGAGGAGAATGGACTGAGCTTTGTTCACATGAGATGACCATCTACAATTA
TGAAGCATGAGCCAATCCAGCTGACCACAGGGTCCATCAGGTAACCCCACAGACACACTTTATTTCC
ORF - retro_btau_1541 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.99 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSHGHSHGGGGCHCAAEREEPPEQRGLAYGLYLRIDLERLQCLNESREGSGRGVFKPWEERTDRSKFVES |
| .SHGHS..G.GC.CAA.REEPP.QRGL..GLYL..DLE..QCL.ES.EGSG.GVF.PWEE.TDRSKFVES | |
| Retrocopy | LSHGHS--GDGCCCAAKREEPP*QRGLTFGLYLLFDLEQSQCLKESHEGSGPGVFRPWEELTDRSKFVES |
| Parental | DADEELLFNIPFTGNVKLKGIIIMGEDDDSHPSEMRLYKNIPQMSFDDTDREPDQTFSLNRDLTGELEYA |
| DADEEL..NIP.TGNVKLKGIIIMG..DDSHPSEMRLY.NIPQMSFDD.D.EPDQTFSLN.DLTGELEYA | |
| Retrocopy | DADEELMLNIPCTGNVKLKGIIIMGDNDDSHPSEMRLYRNIPQMSFDDRDKEPDQTFSLNWDLTGELEYA |
| Parental | TKISRFSNVYHLSIHISKNFGADTTKVFYIGLRGEWTELRRHEVTICNYEASANPADHKVHQVTPQTHFI |
| T.IS.FSN..HLSIHISK.FGADTTKVFYIGLRGEWTEL..HE.TI.NYEA.ANPADH.VHQVTPQTHFI | |
| Retrocopy | TEISHFSNICHLSIHISKKFGADTTKVFYIGLRGEWTELCSHEMTIYNYEA*ANPADHRVHQVTPQTHFI |
| Parental | S |
| S | |
| Retrocopy | S |
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 | 20 .62 RPM |
| ERP005899_muscle | 0 .11 RPM | 15 .15 RPM |
| SRP017611_brain | 0 .05 RPM | 56 .09 RPM |
| SRP017611_kidney | 0 .06 RPM | 22 .11 RPM |
| SRP017611_liver | 0 .00 RPM | 10 .80 RPM |
| SRP030211_testis | 0 .07 RPM | 52 .02 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1541 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1541 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1541 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 | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000021620 | 2 retrocopies |
retro_btau_1541 , retro_btau_939,
|
| Tarsius syrichta | ENSTSYG00000007837 | 1 retrocopy |