RetrogeneDB ID: | retro_sscr_1200 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | X:69994596..69995693(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | AKT2 | ||
| Ensembl ID: | ENSSSCG00000002989 | ||
| Aliases: | AKT2, PRKBB | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_sscr_1200
GGGGAGTACATCAAAACCTGGCTGCCCCAGTACTTCCTCCCAAAGAATGACACACCTTCATCAGCTACAAGGAGTGGCTG
CAGGACATGGAGCAGCGGGAGTCTCCCCTCAACTACTTCTCTGGCTCAATGCCAGCTGATGAAGACTAAGCAGTCACAGC
CCAACACCATCATCTGCTGCCTACAGTGGACCATGGCCATCCAGCACATATTTCATGTGGAGATGTCCAAGGAGTGGAAG
GAGTGGACGACTACCATCCAGATGGTGGCTGACGAGCTCAAGCAGCAGGGGGAAGAGATGATGGACTTCCAGTCGGGCTG
TCCCAGCAAGGACTTGTGGGCAGAGGAGATGGAGTTGTCCCTGTATAAGCCCAAACACCTCGTGACCATGAACGAGTTTG
AGTACCTGAAGCTGCTGGGCAAAGGTACCTTCAGGAAGGTGATCCTGGCAAAGGAGGAGGCCACCAGCAGCTACTACACC
ATGAAGATCCTGAAGAAAGAGGTAATTGTGGCCAGGGACGAGGTGGCCCACATGCTCACAGAGAACTGCATCCTCTAGAA
CTTCCAGCACCCCTTCCAGATGGCCCTGAAGTGCTCCTTCCAGACCTACGATTGCCTGTGCTTCATCATGGAGTATGCCA
ACAGGGATGAGCTCTTCTTCCACCTGTCCTGGGAGCAGGTGTTCCCTGAAGATGGGGGCCAGCTTCTATGGTGCTGAGAT
TGTGTCAGCCCTGGACTACTTGCACTCTGAGAAGGATATGGTGCACCAGGACCTCAAGCTGGAGAACCTCATGCTGGACA
AGGACAGGCACATCAAGATCATTGACTTCAGGCTCTGCAAGGAGGGCATCAAGGATAGTGCCACCATGAAGACATTCTGT
GGGATGCCGGAGTACCTGGTCACCGAGGTGTAGGAGGACAACAACTATGGCCAGGCAGTTGTCTGGTGGGGTGTGGGTGT
GGTCATGTATGAGATAATGTGCAGCCACCTGCCTTTTCTACAACCAGGACCATGAGAAGCTCTTCAAACTCATTCTCATG
AAGGAGATCCGCTTTCCGTGCATGCTCAGCCTTGAGGCCAAGTCTCTGCTCCAAGGA
ORF - retro_sscr_1200 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.34 % |
| Parental protein coverage: | 76.99 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | GEYIKTWRPRYFLLKSDG-SFIGYKERPEAPDQTLPPLNNF-SVAECQLMKTERPRPNTFVIRCLQWTTV |
| GEYIKTW.P.YFL.K.D...FI.YKE......Q...PL.N..S.A.CQLMKT....PNT..I.CLQWT.. | |
| Retrocopy | GEYIKTWLPQYFLPKNDT<TFISYKEWLQDMEQRESPL-NY>SLAQCQLMKTKQSQPNT-IICCLQWTMA |
| Parental | IERTFHVDSPDEREEWMRAIQMVANSLKQRGAGEDPMDYKCGSPSDSSAAEEMEVAVSKARAKVTMNDFD |
| I...FHV....E..EW...IQMVA..LKQ.G..E..MD...G.PS....AEEME....K....VTMN.F. | |
| Retrocopy | IQHIFHVEMSKEWKEWTTTIQMVADELKQQG--EEMMDFQSGCPSKDLWAEEMELSLYKPKHLVTMNEFE |
| Parental | YLKLLGKGTFGKVILVREKATGRYYAMKILRKEVIIAKDEVAHTVTESRVLQNTRHPFLTALKYAFQTHD |
| YLKLLGKGTF.KVIL..E.AT..YY.MKIL.KEVI.A.DEVAH..TE...L.N..HPF..ALK..FQT.D | |
| Retrocopy | YLKLLGKGTFRKVILAKEEATSSYYTMKILKKEVIVARDEVAHMLTENCIL*NFQHPFQMALKCSFQTYD |
| Parental | RLCFVMEYANGGELFFHLSRERVFTEE-RARFYGAEIVSALEYLHS-RDVVYRDIKLENLMLDKDGHIKI |
| .LCF.MEYAN..ELFFHLS.E.VF.E...A.FYGAEIVSAL.YLHS..D.V..D.KLENLMLDKD.HIKI | |
| Retrocopy | CLCFIMEYANRDELFFHLSWEQVFPED>GASFYGAEIVSALDYLHSEKDMVHQDLKLENLMLDKDRHIKI |
| Parental | TDFGLCKEGISDGATMKTFCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLP-FYNQDHERLFE |
| .DF.LCKEGI.D.ATMKTFCG.PEYL..EV.EDN.YG.AV.WWG.GVVMYE.MC..LP.FYNQDHE.LF. | |
| Retrocopy | IDFRLCKEGIKDSATMKTFCGMPEYLVTEV*EDNNYGQAVVWWGVGVVMYEIMCSHLP>FYNQDHEKLFK |
| Parental | LILMEEIRFPRTLSPEAKSLLAG |
| LILM.EIRFP..LS.EAKSLL.G | |
| Retrocopy | LILMKEIRFPCMLSLEAKSLLQG |
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 .13 RPM | 148 .26 RPM |
| SRP014902_testis | 0 .14 RPM | 183 .46 RPM |
| SRP018288_heart | 0 .08 RPM | 41 .05 RPM |
| SRP018288_kidney | 0 .00 RPM | 55 .16 RPM |
| SRP018288_liver | 0 .00 RPM | 85 .07 RPM |
| SRP018288_lung | 0 .00 RPM | 96 .84 RPM |
| SRP018856_adipose | 0 .00 RPM | 860 .84 RPM |
| SRP035408_brain | 0 .00 RPM | 29 .95 RPM |
| SRP035408_liver | 0 .00 RPM | 36 .55 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_1200 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_1200 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_1200 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000014574 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000004056 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000002989 | 2 retrocopies |
retro_sscr_1164, retro_sscr_1200 ,
|