RetrogeneDB ID: | retro_fcat_43 | ||
Retrocopy location | Organism: | Cat (Felis catus) | |
| Coordinates: | D2:5519303..5521235(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSFCAG00000028055 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CSTF2 | ||
| Ensembl ID: | ENSFCAG00000007000 | ||
| Aliases: | None | ||
| Description: | cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa [Source:HGNC Symbol;Acc:2484] |
Retrocopy-Parental alignment summary:
>retro_fcat_43
ATGTCGAGTTTAGCGGTGAGAGACCCGGCGATGGATCGGTCACTGCGTTCCGTGTTCGTGGGGAACATTCCGTATGAGGC
AACCGAGGAGCAGCTGAAGGACATTTTCTCGGAGGTCGGTTCTGTGGTCAGTTTCCGGCTGGTGTACGACCGGGAGACGG
GCAAGCCCAAGGGCTATGGCTTCTGCGAGTACCAGGACCAGGAGACCGCGCTGAGCGCCATGCGCAACCTCAACGGGCGC
GAGTTCAGCGGCCGGGCGCTGCGGGTGGACAACGCGGCCAGCGAGAAGAACAAGGAGGAGCTCAAGAGCCTGGGGCCCGC
GGCGCCCATCATCGACTCGCCCTACGGGGACCCCATCGACCCGGAAGACGCCCCCGAGTCCATCACCAGGGCGGTCGCCA
GTCTGCCCCCCGAGCAGATGTTCGAGCTCATGAAGCAGATGAAGCTGTGCGTGCAGAACAGCCACCAGGAAGCGCGAAAT
ATGCTGCTTCAGAACCCCCAGCTGGCCTATGCGCTGCTGCAGGCCCAGGTGGTGATGAGAATAATGGACCCGGAGATTGC
TCTGAAAATCCTGCACCGCAAGATCCACGTCACCCCGCTCATCCCGGGCAAGTCTCAGCCCGTGTCCGGCCCCGGCCCCG
GCCCCGGCCCGGGGCTGTGCCCGGGACCCAGTGTCCTGCTGAACCAGCAGAACCCGCCAGCCCCTCAGCCGCAGCATATG
GCCAGACGGCCAGTGAAAGACATTCCTCCTCTGATGCAGACCCCTATCCAGGGCGGGATCCCAGCCCCGGGGCCGATGCC
AGCTGCGGTTCCCGGACCCGGGCCTGGTTCCCTAACTCCCGGGGGAGGCATGCAGCCCCAGGTTGGGATGCCGGGCGTCG
GCCCAGTGCCTTTAGAGCGGGGACAGGTGCAGATGTCGGATCCCCGAGCTCCTCTACCTCGTGGACCCATGACTGCCGGT
GGCCTGCCTCCTCGAGGGCTGTTAGGAGATGCTCCAAACGACCCCCGTGGAGGGACTTTGCTTTCAGTCACCGGGGAGGT
AGAGCCCAGAGGCTATCTTGGCCCACCTCATCAGGGCCCCCCCATGCACCACGCCTCTGGTCACGACGGCCGGGGCCCTT
CCTCCCATGAGATGAGGGGAGGGCCATTAGCAGATCCCAGACTGCTAATTGGAGAGCCCAGAGGACCCATGATAGATCAA
AGGGGTCTCCCAATGGATGGTAGAGGAAGTAGAGATTCTCGAGGGATGGAGACTCGAGCCATGGAGACGGAAGTCTTGGA
GACCCGAGTAATGGAGAGAAGAGGAATGGAGACCTGTGCAATGGAAACCAGAGGGATGGAAGCGAGAGGCATGGATGGAA
GAGGAATGGAGCTAAGGGGCCCTGGCCCCAGCTCCAGAGGCCCTATGACTGGTGGAATCCAGGGTCCTGGTCCCATTAAT
ATGGGGGCAGGTGGTCCTCAGGGACCCAGACAGGTCTCGAGCATTTCAGGGGTGGGAAATCCTGGAGCGGGCATGCAGGG
GGCAGGCATACAAGGAACGGGCATGCAGGGGGCGGGCATACAAGGAACGGGCATGCAGGGGGCGGGCATACAAGGAACGG
GCATGCAGGGGGCGGGCATACAAGGAACGGGCATGCAGGGGGCGGGCATACAAGGAACGGGCATGCAGGGGGCGGGCATA
CAAGGAGCAGGCATGCAGGGGGCGGGCATACAAGGAGTGGGCATGCAGGGGGCGGGTAAGCAAGGTGGAGGCCAGCCGAG
CAGTTTTAGCCCTGGGCAGAGCCAGGTAACTCCGCAGGATCAAGAGAAGGCAGCTCTGATCATGCAGGTTCTCCAACTGA
CTGCAGATCAGATCGCCATGCTGCCTCCTGAGCAAAGGCAGAGCATCCTGATTTTAAAGGAACAAATTCAGAAATCTACT
GGAGCTTCTTGA
ORF - retro_fcat_43 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.12 % |
| Parental protein coverage: | 84.2 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAGLTVRDPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA |
| M..L.VRDPA.DRSLRSVFVGNIPYEATEEQLKDIFSEVG.VVSFRLVYDRETGKPKGYGFCEYQDQETA | |
| Retrocopy | MSSLAVRDPAMDRSLRSVFVGNIPYEATEEQLKDIFSEVGSVVSFRLVYDRETGKPKGYGFCEYQDQETA |
| Parental | LSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAPVIESPYGETISPEDAPESISKAVASLPPEQM |
| LSAMRNLNGREFSGRALRVDNAASEKNKEELKSLG..AP.I.SPYG..I.PEDAPESI..AVASLPPEQM | |
| Retrocopy | LSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGPAAPIIDSPYGDPIDPEDAPESITRAVASLPPEQM |
| Parental | FELMKQMKLCVQNSPQEARNMLLQNPQLAYALLQAQVVMRIVDPEIALKILHRQTNIPTLIAGNPQ---- |
| FELMKQMKLCVQNS.QEARNMLLQNPQLAYALLQAQVVMRI.DPEIALKILHR......LI.G..Q.... | |
| Retrocopy | FELMKQMKLCVQNSHQEARNMLLQNPQLAYALLQAQVVMRIMDPEIALKILHRKIHVTPLIPGKSQPVSG |
| Parental | PVHSAGPG--SGSSVSMSQQNPQAPQAQSLGGMHVNGAPPLMQASMQAGVPAPGQIPATVTGPGPGSLAP |
| P....GPG...G.SV...QQNP.APQ.Q......V...PPLMQ...Q.G.PAPG..PA.V.GPGPGSL.P | |
| Retrocopy | PGPGPGPGLCPGPSVLLNQQNPPAPQPQHMARRPVKDIPPLMQTPIQGGIPAPGPMPAAVPGPGPGSLTP |
| Parental | GGGMQAQVGMPGSGPVSIERGQVPMQDPRAAMQRGPLPANVPTPRGLLGDAPNDPRGGTLLSVTGEVEPR |
| GGGMQ.QVGMPG.GPV..ERGQV.M.DPRA...RGP..A....PRGLLGDAPNDPRGGTLLSVTGEVEPR | |
| Retrocopy | GGGMQPQVGMPGVGPVPLERGQVQMSDPRAPLPRGPMTAGGLPPRGLLGDAPNDPRGGTLLSVTGEVEPR |
| Parental | GYLGPPHQGPPMHHVPGHDSRGPPPHEMRGGPLAEPRPLMAEPRGPMLDQRGPPLDGRGGRDPRGIDTRG |
| GYLGPPHQGPPMHH..GHD.RGP..HEMRGGPLA.PR.L..EPRGPM.DQRG.P.DGRG.RD.RG..TR. | |
| Retrocopy | GYLGPPHQGPPMHHASGHDGRGPSSHEMRGGPLADPRLLIGEPRGPMIDQRGLPMDGRGSRDSRGMETRA |
| Parental | MEARAMEARGLDARGLEARAMEARAMEARAMEARAMEARAMEVRGIEARSMDTRGPVPGPRGPIPSGIQG |
| ME....E.R....RG.E..AME.R.MEAR.M..R.ME.R.....G...R...T.G...GP.GPI..G..G | |
| Retrocopy | METEVLETRVMERRGMETCAMETRGMEARGMDGRGMELRG---PGPSSRGPMTGG-IQGP-GPINMGAGG |
| Parental | P |
| P | |
| Retrocopy | P |
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 |
|---|---|---|
| SRP017611_brain | 16 .76 RPM | 10 .79 RPM |
| SRP017611_kidney | 8 .55 RPM | 9 .38 RPM |
| SRP017611_liver | 6 .27 RPM | 7 .38 RPM |
Felis catus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_fcat_43 retrocopy.
Felis catus was not studied using FANTOM5 data.
retro_fcat_43 was not experimentally validated.
Retrocopy orthology:
Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000009325 | 1 retrocopy | |
| Felis catus | ENSFCAG00000007000 | 1 retrocopy |
retro_fcat_43 ,
|
| Macropus eugenii | ENSMEUG00000011186 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000013556 | 1 retrocopy |