RetrogeneDB ID: | retro_ecab_19 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 1:42306179..42307928(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSECAG00000004701 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CSTF2 | ||
| Ensembl ID: | ENSECAG00000009325 | ||
| Aliases: | None | ||
| Description: | cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa [Source:HGNC Symbol;Acc:2484] |
Retrocopy-Parental alignment summary:
>retro_ecab_19
GAGGTTGGTTCTGTTGTCAGTTTCCGGCTGGTATACGATCGAGAGACGGGAAAACCCAAGGGGTATGGCTTCTGCGAGTA
TCAAGACCAGGAGACCGCGCTTAGTGCCATGCGGAACCTTAATGGGCGGGAGTTCAGCGGGAGAGCGCTTCGGGTGGACA
ATGCTGCCAGTGAAAAGAACAAGGAGGAGTTAAAGAGCCTAGGGCCTGCAGCGCCCATCATTGACTCCCCCTACGGGGAC
CCCATCGATCCGGAAGATGCCCCAGAATCAATTACCAGGGCAGTTGCTAGTCTCCCCCCGGAGCAAATGTTTGAGCTGAT
GAAGCAGATGAAGCTGTGTGTCCAAAACAGTCACCAGGAAGCTCGAAACATGTTACTTCAAAACCCCCAACTGGCTTACG
CCCTGTTACAGGCGCAAGTAGTGATGAGGATCATGGATCCAGAGATTGCTTTGAAAATTCTGCATCGCAAGATACATGTC
ACACCGCTCATCCCAGGCAAATCTCAGCCTGTCTCTGGCCCTGGCCCTGGGATCTGCCCAGGACCTAATGTTCTACTGAA
CCAGCAGAATCCTCCAGCCCCTCAGCCTCAGCATTTGGCTAGAAGACCTGTGAAAGACATCCCTCCTCTGATGCAGACCC
CTATCCAGGGTGGAATTCCAGCCCCAGGGCCAATACCAACTGGGGTTCCCGGACCTGGTCCTGGTTCCTTAACTCCTGGT
GGAGCAATGCAGCCCCAAGTTGGAATGCCAGGGGTTGGTCCTGTGCCTTTAGAGCGGGGACAGGTGCAGATGTCGGATCC
TAGAGCTCCTATGCCTCGTGGACCCATGACTGCTGGTGGCCTGCCTCCTCGAGGACTGTTAGGAGATGCACCAAATGACC
CACGTGGAGGGACTTTGCTCTCAGTCACTGGAGAAGTAGAGCCCAGAGGCTATCTTGGCCCACCTCATCAGGGTCCCCCT
ATGCACCATGCCTCTGGTCATGACAGCCGTGGCCCTTCCTCACATGAGATGAGGGGAGGGCCATTAGCAGATCCCAGAAT
GCTAATTGGAGAGCCCAGAGGACCCATGATGGATCAAAGGGGTCTACCTTTGGATGGTAGAGGTAGTAGAGATTCTCGAG
GGATGGAGACTCGAGCCATGGAAACTGAGGTCTTAGAGACACGAGTAATGGAGAGAAGAGGAATGGAGACCTGTGCAATG
GAAGCCAGAGGGATGGAAGCAAGAGGCATGGATGCAAGAGGAATGGAGATAAGGGGCCCTGGCCCCAGTTCGAGAGGCCC
TATGACTGGTGGAATCCAGGGTCCTGGTCCCATTAATATGGGGGCAGGTGGTCCTCAGGGACCCAGACAGGTCCCAAGCA
TTTCAGGGGTGGGAAATCCTGGAGCTGGCATGCAGGGGGCAGGCATACAAGGAGCAGGCATGCAGGGAGCGGGCATGCAG
GGATCGGGCATGCAGGGAGCAGGCATGCAGGGAGCGGGCATGCAGGGAGCGGGCATACAAGGAGTGGGCATGCAGGGGGC
CGGCATACAAGGAACGGGCATGCAGGGGGCGGGCAAGCAAGGTGGAGGCCAGCCTAGCAGTTTTAGTCCTGGGCAGAGCC
AAGTAACTCCCCAGGATCAAGAAAAGGCAGCTTTGATCATGCAGGTTCTTCAACTGACTGCAGATCAGATTGCCATGCTG
CCTCCTGAGCAAAGGCAGAGCATCCTGATTTTAAAGGAACAAATCCAGAAGTCTACTGGAGCTTCTTGA
ORF - retro_ecab_19 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.97 % |
| Parental protein coverage: | 84.75 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | EVGPVVSYLLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTG |
| EVG.VVS..LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLG.. | |
| Retrocopy | EVGSVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGPA |
| Parental | APVIESPYGETISPEDAPESISKAVASLPPEQMFELMKQMKLCVQNSPQEARNMLLQNPQLAYALLQAQV |
| AP.I.SPYG..I.PEDAPESI..AVASLPPEQMFELMKQMKLCVQNS.QEARNMLLQNPQLAYALLQAQV | |
| Retrocopy | APIIDSPYGDPIDPEDAPESITRAVASLPPEQMFELMKQMKLCVQNSHQEARNMLLQNPQLAYALLQAQV |
| Parental | VMRIVDPEIALKILHRQTNIPTLIAGNPQPVHSTGPG--SGSNVSMNQQNPQAPQAQSLGGMHVNGAPPL |
| VMRI.DPEIALKILHR......LI.G..QPV...GPG...G.NV..NQQNP.APQ.Q.L....V...PPL | |
| Retrocopy | VMRIMDPEIALKILHRKIHVTPLIPGKSQPVSGPGPGICPGPNVLLNQQNPPAPQPQHLARRPVKDIPPL |
| Parental | MQASMQAGVPTPGQMPASVTGPGPGALAPGGGMQAQVGMPGSGPVSMERGQVPMQDPRAAMQRGPLPANV |
| MQ...Q.G.P.PG..P..V.GPGPG.L.PGG.MQ.QVGMPG.GPV..ERGQV.M.DPRA.M.RGP..A.. | |
| Retrocopy | MQTPIQGGIPAPGPIPTGVPGPGPGSLTPGGAMQPQVGMPGVGPVPLERGQVQMSDPRAPMPRGPMTAGG |
| Parental | PTPRGLLGDAPNDPRGGTLLSVTGEVEPRGYLGPPHQGPPMHHVPGHDSRGPPPHEMRGGPLAEPRPLMA |
| ..PRGLLGDAPNDPRGGTLLSVTGEVEPRGYLGPPHQGPPMHH..GHDSRGP..HEMRGGPLA.PR.L.. | |
| Retrocopy | LPPRGLLGDAPNDPRGGTLLSVTGEVEPRGYLGPPHQGPPMHHASGHDSRGPSSHEMRGGPLADPRMLIG |
| Parental | EPRGPMLDQRGPPLDGRGGRDPRGMDARGMEARAMEARGLDARGLEARAMEARAMEARAMEARAMEARAM |
| EPRGPM.DQRG.PLDGRG.RD.RGM..R.ME....E.R....RG.E..AMEAR.MEAR.M.AR.ME.R.. | |
| Retrocopy | EPRGPMMDQRGLPLDGRGSRDSRGMETRAMETEVLETRVMERRGMETCAMEARGMEARGMDARGMEIRGP |
| Parental | EVRGMEARSMDTRGPVPGPRGPIPSGIQGPSPI-NMGAVG-PQGSRQVPVMQGAAMQGASIQGGGQPGGF |
| .............GP..GP......G.QGP........VG.P....Q....QGA.MQGA..QG.G..G.. | |
| Retrocopy | GPSSRGPMTGGIQGP--GPINMGAGGPQGPRQVPSISGVGNPGAGMQGAGIQGAGMQGAGMQGSGMQGAG |
| Parental | SPG |
| ..G | |
| Retrocopy | MQG |
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 |
|---|---|---|
| SRP021940_articular_cartilage | 29 .46 RPM | 5 .25 RPM |
| SRP021940_cerebellum | 43 .26 RPM | 12 .57 RPM |
| SRP021940_embryo | 65 .08 RPM | 16 .95 RPM |
| SRP021940_placental_villous | 20 .50 RPM | 10 .83 RPM |
| SRP021940_synovial_membrane | 24 .30 RPM | 10 .05 RPM |
| SRP021940_testis | 68 .80 RPM | 9 .40 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_19 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_19 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_19 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000008257 | 1 retrocopy | |
| Equus caballus | ENSECAG00000009325 | 1 retrocopy |
retro_ecab_19 ,
|
| Felis catus | ENSFCAG00000007000 | 1 retrocopy | |
| Macropus eugenii | ENSMEUG00000011186 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000013556 | 1 retrocopy |