RetrogeneDB ID: | retro_dnov_932 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_12312:49134..50318(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PLEKHM3 | ||
| Ensembl ID: | ENSDNOG00000004208 | ||
| Aliases: | None | ||
| Description: | pleckstrin homology domain containing, family M, member 3 [Source:HGNC Symbol;Acc:34006] |
Retrocopy-Parental alignment summary:
>retro_dnov_932
TCTTTTCATGTCTCTCACTTCACTAGACCATCTTTTCTGTCACCATCATCAAATAATGTAGAAGATGCTCAAGGAAATAC
TGAACACAAGCAGACATTCCCAAACATTCTGAAGAAGGGTTACCTGGAGTTTAGGAAGGACCATGATAGTTATTGGCAAA
GCTGTTATGCAGAACTATCACCCTACAACTTAAACTACTTTAATCTCTACAGCAGGGCAAATCAAAACCTCTGTGCCACA
TATCAACTTTCACACTTTCAGACCATACCTGTTTTGGGCAACCTTGAGGCCAGAATAGTGGATACCATCTTGTATGAAAA
CATTCAGCTACAGCTCAAGGCAGAGTCACCATGGGAGGCTTTGGACTGGGGCTAGAAGCTTTGGGAAGGTGTGCATACTG
CTGTGCTTGGTTACATGGGACAGGAGGATAAGCTGGCAAACTCACCAGACCTTGGTCCTAATGCTGACCGTACACAGAAT
CATTGTTTACAGAAGAAATCCAGAGGGTTGCTGCCATCATCGCCTGCCTCAGATAGCCCCAAACAGTACCAAAACATCCT
CAAATCAGGGACGCTCTGCAGGCTAACTGTCCAAAACAACTGGAAGGCATTTATGTTTGTGCTGAGCACAGCCTGCCTTA
CGGATTTTCAGCCTGGCAAGCTAGACGAGGGTCTCCTGCTGAGCTACAATGTGGATGTGTGTCTGGCTGTCCAGATAGAC
AACCTGGATGATTGTGACTCTTTCAAGTCATTTTTCCACAAGATATCCTCTATCTCCATGCTGAGACCTGACAAAGAGCT
CAGGAATGGATGGAGGCTCTGAAAAGAAGCTACCAACACTGCAAGGAGTTCAGAGCAAAATCTGCAAGTGACACTGAGGA
ACAAATCCAAGGATCAGATTGGTGGGCACAAACTCAGGAAGAACAAACATCAGTCCATGACCACCAGCTTCCTGAGCATT
CTGACAACTTTGTCTCTAGAATGAAGACTTACTGCTCAGAGTTTCAAATGTGAAGGAAGCCAGTGATGCACAGGTCTTTC
CAATGAGAAAGCCAAGGTGTGTGATTACAGTGGGTGCTATTACTGAAGCGGCTGCCATGTGGACGACAGTTTTCTTATCC
CAGCATACATTGTCCACAACTGGGACACTTCTAAATATAAGTGTCTAAGCAGGCCAAAGAGTTT
ORF - retro_dnov_932 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.21 % |
| Parental protein coverage: | 52.04 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | SLHGPHFTRPSFLLPSSNKVEDAQGNTENKQTFPNILKKGYLEIRKDHDSYWQSCYAELSPYNLNFFNLD |
| S.H..HFTRPSFL.PSSN.VEDAQGNTE.KQTFPNILKKGYLE.RKDHDSYWQSCYAELSPYNLN.FNL. | |
| Retrocopy | SFHVSHFTRPSFLSPSSNNVEDAQGNTEHKQTFPNILKKGYLEFRKDHDSYWQSCYAELSPYNLNYFNLY |
| Parental | SSANQNLCATYQLTHFQSISVLGNLEARIVDTVLYDNTQLQLKAESPWEALDWGQKLWEVVHMAVPGYMG |
| S.ANQNLCATYQL.HFQ.I.VLGNLEARIVDT.LY.N.QLQLKAESPWEALDWG.KLWE.VH.AV.GYMG | |
| Retrocopy | SRANQNLCATYQLSHFQTIPVLGNLEARIVDTILYENIQLQLKAESPWEALDWG*KLWEGVHTAVLGYMG |
| Parental | RQDKLANSSDLGLNADCTQNHCLQKKSRGLLPSSPVLDSPKQYQNILKSGTLYRLTVQNNWKAFTFVLSR |
| ..DKLANS.DLG.NAD.TQNHCLQKKSRGLLPSSP..DSPKQYQNILKSGTL.RLTVQNNWKAF.FVLS. | |
| Retrocopy | QEDKLANSPDLGPNADRTQNHCLQKKSRGLLPSSPASDSPKQYQNILKSGTLCRLTVQNNWKAFMFVLST |
| Parental | ACLMAFQPGKLDEDPLLSYNVDVCLAVQIDNLDDCDSCFQVIF-PQDILRLRAETRQRAQEWMEAL-KTA |
| ACL..FQPGKLDE..LLSYNVDVCLAVQIDNLDDCDS.F...F.PQDIL.L.AET.QRAQEWMEAL.K.A | |
| Retrocopy | ACLTDFQPGKLDEGLLLSYNVDVCLAVQIDNLDDCDS-FKSFF<PQDILYLHAET*QRAQEWMEAL>KEA |
| Parental | ANTARSSEQNLQVTLRNKSKDQMGAHELRKNKRQSVTTSFLSILTTLSLERGLTAQSFKCAGCQRCIGLS |
| .NTARSSEQNLQVTLRNKSKDQ.G.H.LRKNK.QS.TTSFLSILTTLSLE..LTAQSFKC.G.Q.C.GLS | |
| Retrocopy | TNTARSSEQNLQVTLRNKSKDQIGGHKLRKNKHQSMTTSFLSILTTLSLE*RLTAQSFKCEGSQ*CTGLS |
| Parental | NGKAKVCNYSGWYYCSSCHVDDSFLIPARIVHNWDTSKYK-VSKQAKEF |
| N.KAKVC.YSG.YY.S.CHVDDSFLIPA.IVHNWDTSKYK.VSKQAKEF | |
| Retrocopy | NEKAKVCDYSGCYY*SGCHVDDSFLIPAYIVHNWDTSKYK<VSKQAKEF |
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 |
|---|---|---|
| SRP012922_ascending_colon | 0 .00 RPM | 5 .25 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 8 .80 RPM |
| SRP012922_heart | 0 .00 RPM | 2 .32 RPM |
| SRP012922_kidney | 0 .00 RPM | 0 .55 RPM |
| SRP012922_liver | 0 .00 RPM | 1 .55 RPM |
| SRP012922_lung | 0 .00 RPM | 4 .73 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 1 .73 RPM |
| SRP012922_spleen | 0 .00 RPM | 5 .61 RPM |
Dasypus novemcinctus was not studied using ChIP-Seq data.
Dasypus novemcinctus was not studied using EST data.
Dasypus novemcinctus was not studied using FANTOM5 data.
retro_dnov_932 was not experimentally validated.
Retrocopy orthology:
Dasypus novemcinctus 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 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000004208 | 1 retrocopy |
retro_dnov_932 ,
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