RetrogeneDB ID: | retro_sscr_619 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 2:57408084..57409356(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SAMD4B | ||
| Ensembl ID: | ENSSSCG00000010706 | ||
| Aliases: | None | ||
| Description: | sterile alpha motif domain containing 4B [Source:HGNC Symbol;Acc:25492] |
Retrocopy-Parental alignment summary:
>retro_sscr_619
TTCCCCATGACTGACTGTGAATCCCTCTCAACCCACAGCAGTGTGGCCTCCTCTAGTTGTGAGCAGACCAAGGAGCAGGG
CTGCAGCTAGAACACATTCTAGGAGGATAGCAGTGGCATGAAAGACATGCCCCTGTGGCTCAAGAGCCTCTACCTGCACA
AGTATGTGGCCCTTTTCTCACAGATGAGTGATGAGGAGATGATGACACTGACTGAGAAGCACACAGAGTCCTAGAATGTC
ACTAAAGGTGCCTGCCTTAAGATAGTCTTGAACATCCAGAGGTGCATGAGAAGCAGAGCATCCTCAAATCCCTAGAGAAG
GATGTGCTGGAAGGTGGAAATCTGCATAATGTTCTGAAGGAGCTTAAGCAGATCATAATCACCCTCATGAATGCCTACAG
TGTCTTCCAGGCCACTCTGGCTACTACCACCACCACCACTCCTCCTGCCAAAGATGGGGGCAGGGAGTGGGGAGAGGAAG
CTTCCACTGTATGGTGCTGAGCCTCCCTTGGCTCATCTTGGCACAGACAAGGGCAGTGAGGCCAAGGACCCTCTAGCTGC
AGAGAGCTTCCTCCATCCACATGCTCTGGTTTCCGCTGATGGCAGTGAGCCAGCCCTAGTTCCTGTCTCTGATGGAGACA
TCCCCAGCTGGTTTACAGAGATGAAGAACAAATTGTGAACCCAGCTGCTGATGTCCCATCCAGACAAGGAGAACATCAGC
AGTTACCTCCATGTAATTGAAAATTGCCTGAATCATGAGGCTTTCAAGGAGACACAGAAGAAATGGCTGCTGTCCTAGAA
AGAGCAAGTGTTAAATCTCCTCTGGATCTTCCCATGCAAAGCTGCACTAGAGATTCAGAACTTCCAGCAGCAGAAAGGTT
AGACATTCAGCCACAACTCACTCCTTATAGCTGGCTCTGTGGAGATGGGGGTGGCCCAGCAGACCCATAAACAGTTCCCA
ATGCCTTCCTGGGTCCTTCTGCCTGGCAGGATAGGTCTTCAGAGCCTCCCAGGCATATCTCCCCATCAATATCTACCCCC
AAACATGCCCTCACCAACTCCAACCTTGGGGGCCACTATCATCACAACCTGTGGTTTATCAATCTGGGAGGCAGTAAAAG
ATGCCCAGCCAGAGCTGCAGCTCTCTGCAGTGCATCCACTCATTCACAGTCCATTCATTCCCCCAGATTACTCTCATATT
CCCTCCAGATTGTCTGGTCCCTGGACCTGACCTTGAGATCAATCCCACCCTGGAGTGTTTTGTTTGAGCATT
ORF - retro_sscr_619 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.65 % |
| Parental protein coverage: | 53.44 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | FTTPDHAPLSPQSSVASSGSEQTEEQGSSRNTFQEDGSGMKDVPSWLKSLRLHKYAALFSQMSYEEMMTL |
| F...D...LS..SSVASS..EQT.EQG.S.NTF.ED.SGMKD.P.WLKSL.LHKY.ALFSQMS.EEMMTL | |
| Retrocopy | FPMTDCESLSTHSSVASSSCEQTKEQGCS*NTF*EDSSGMKDMPLWLKSLYLHKYVALFSQMSDEEMMTL |
| Parental | TEQHLESQNVTKGARHKIALSIQK-LRERQSVLKSLEKDVLEGGNLRNALQELQQIIITPIKAYSVLQAT |
| TE.H.ES.NVTKGA..KI.L.IQ....E.QS.LKSLEKDVLEGGNL.N.L.EL.QIIIT...AYSV.QAT | |
| Retrocopy | TEKHTES*NVTKGACLKIVLNIQR<VHEKQSILKSLEKDVLEGGNLHNVLKELKQIIITLMNAYSVFQAT |
| Parental | VAAGAT-TTP-PAKDGGRGEPPLP--GAESPLAHPGTDKGSEAKDPPAAESFPPPPAPASTDGSEPAPAP |
| .A...T.T.P.P....G.GE..LP..GAE.PLAH.GTDKGSEAKDP.AAESF..P.A..S.DGSEPA..P | |
| Retrocopy | LATTTTTTPP>PKMGAGSGERKLPLYGAEPPLAHLGTDKGSEAKDPLAAESFLHPHALVSADGSEPALVP |
| Parental | VADGDIPSQFTRVMGKVCTQLLVSRPDEENITSYLQLIEKCLTHEAFTETQKKRLLSWKQQVLKLLRTFP |
| V.DGDIPS.FT....K..TQLL.S.PD.ENI.SYL..IE.CL.HEAF.ETQKK.LLS.K.QVL.LL..FP | |
| Retrocopy | VSDGDIPSWFTEMKNKL*TQLLMSHPDKENISSYLHVIENCLNHEAFKETQKKWLLS*KEQVLNLLWIFP |
| Parental | RKAALEMQNYRQQKGWAFGSNSLPIAGSVGMGVARRTQRQFPMPPRALPPGRMGLLSPSGIGG---ISPR |
| .KAALE.QN..QQKG..F..NSL.IAGSV.MGVA..T..QFPMP...L.PGR.GL.S..GI.......P. | |
| Retrocopy | CKAALEIQNFQQQKG*TFSHNSLLIAGSVEMGVAQQTHKQFPMPSWVLLPGRIGLQSLPGISPHQYLPPN |
| Parental | HALTSPSL-GGQGRQNLWFANPGGSN-SMPSQSRSSVQRTHSLPVHSSPQAILMFPPDCPVPGPDLEINP |
| .....P.L.GG....NLWF.N.GGS...MPSQS.SS.Q..HS..VHS.PQ..L.FPPDC.VPGPDLEINP | |
| Retrocopy | MPSPTPTL<GGHYHHNLWFINLGGSK<KMPSQSCSSLQCIHSFTVHSFPQITLIFPPDCLVPGPDLEINP |
| Parental | TLES-LCLSM |
| TLE...CLS. | |
| Retrocopy | TLEC<FCLSI |
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 |
|---|---|---|
| SRP014902_placenta | 0 .00 RPM | 74 .59 RPM |
| SRP014902_testis | 0 .00 RPM | 45 .97 RPM |
| SRP018288_heart | 0 .00 RPM | 15 .48 RPM |
| SRP018288_kidney | 0 .00 RPM | 19 .80 RPM |
| SRP018288_liver | 0 .00 RPM | 9 .59 RPM |
| SRP018288_lung | 0 .00 RPM | 51 .32 RPM |
| SRP018856_adipose | 0 .00 RPM | 27 .20 RPM |
| SRP035408_brain | 0 .00 RPM | 7 .37 RPM |
| SRP035408_liver | 0 .00 RPM | 3 .26 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_619 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_619 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_619 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 | |
|---|---|---|---|
| Sus scrofa | ENSSSCG00000010706 | 1 retrocopy |
retro_sscr_619 ,
|