RetrogeneDB ID: | retro_dnov_1735 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_27981:40455..41367(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LPCAT2 | ||
| Ensembl ID: | ENSDNOG00000006859 | ||
| Aliases: | None | ||
| Description: | lysophosphatidylcholine acyltransferase 2 [Source:HGNC Symbol;Acc:26032] |
Retrocopy-Parental alignment summary:
>retro_dnov_1735
TCTTATAAACTAGAGACCTTCTTTGCAGGTGTTCTCCTGCAGCCAGTGCTGCTCAGGCACCCAAATGACTGGACACAGTG
ACCTGGACCTGGCAGGGGTCATCAGCCTTCCAGGTCTGCATGTTAACCTTGGTCAGCTCTTCACCAGAATGGAGGTTGAG
TTTATGCCTGTTCATAGAAACAAATGATGAAGAGAAAAAAAGACCCAGTCCTTTTTGCCAACACACTAAGAATCACCCTG
GCAACTGGGGAGTGCCTGTGACAGACCACTCTTAGGAGGACTGCAGACTGATATCTGCGGGTCACCTTCAACCACCCATG
GAAGCTGGCTTGATGGAATTTACAAAAATTAGTCAGAAATCGAAGATAAATTGGAATAATATCCATCAGCATTTGGATGA
ATATGCTACAATTGCAATTGCCTCCAGAGGACAAAAGACAGAAATAGAAGAGTTTGCAAGATACTTAAATCTCCGCATTT
CCAAGCTCTTGAGACAATTCTTTGCCCACTTTGACAGGAGTAACAATGTCAGAATAGACTTTAGAGAGCACCGTGATAGG
TTTGACAATCCCATGCAACACTGCAAACACAGAAAAGATTTTGCTTATGTCATTTAGGCTTTTTGACCCTGGTGAGAATG
GTTCCATAACAGAACAGGAGTTAGCTGCTATACTTGGGGCCGCTTTTGGAGTGCTGGATCTTGATGTTTCCAAACTCTTC
CAGGAAATAGCTGGGCAGAACTCAGTGTACATTTCATTCAAAACTTTTGAGAAATTTGATCTGAAGCATCCAGAATATAT
CAAGTTATTTAGTTCATACCTAGATTTCCAGGCAGCCCATATATTTCCATTACAAGAAGTACAAGTTTAATCACTGTATT
CAAATGTTAAAGTCAGTCCTGAAAATAATGAA
ORF - retro_dnov_1735 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.77 % |
| Parental protein coverage: | 56.07 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | TFKPGAFIPGVPVQPILLRY-PNKLXXXXXXXXXXXXIQLCVLTFC-QPFTKVEIEFMPVQ-VPNDEEKN |
| ..K...F..GV..QP.LLR..P..L.............Q.C.LT...Q.FT..E.EFMPV....NDEEK. | |
| Retrocopy | SYKLETFFAGVLLQPVLLRH<PK*LDTVTWTWQGSSAFQVCMLTLV<QLFTRMEVEFMPVH>ETNDEEKK |
| Parental | DPVLFASRVRSFMADALGIPVTDHTYEDCRLMISAGQLTLPMEAGLVEFTKISRKLKLDWDGIRKHLDEY |
| .P..F............G.PVTDH..EDCRL.ISAG.L..PMEAGL.EFTKIS.K.K..W..I..HLDEY | |
| Retrocopy | RPSPFCQHTKNHPGN-WGVPVTDHS*EDCRL-ISAGHLQPPMEAGLMEFTKISQKSKINWNNIHQHLDEY |
| Parental | AAIASSSKGGRIGIEEFAEYLKLPVSDVLRQLFALFDRXHDGSIDFREY-VIGLAVLCNPANTEEIIQVA |
| A.IA..S.G....IEEFA.YL.L..S..LRQ.FA.FDR.....IDFRE..VIGL...CN.ANTE.I.... | |
| Retrocopy | ATIAIASRGQKTEIEEFARYLNLRISKLLRQFFAHFDRSNNVRIDFREH>VIGLTIPCNTANTEKILLMS |
| Parental | FKLFDVDEDGYITEEEFSTILQASLGVPDLDVSGLFKEIAQGDSV--SYEEFKSFALKHPEYAKIFTTYL |
| F.LFD..E.G.ITE.E...IL.A..GV.DLDVS.LF.EIA...SV..S...F..F.LKHPEY.K.F..YL | |
| Retrocopy | FRLFDPGENGSITEQELAAILGAAFGVLDLDVSKLFQEIAGQNSVYISFKTFEKFDLKHPEYIKLFSSYL |
| Parental | DLQTCHVFSLPKEVQAAPSVASNKVSPENHE |
| D.Q..H.F.L..EVQ........KVSPEN.E | |
| Retrocopy | DFQAAHIFPL-QEVQV*SLYSNVKVSPENNE |
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 | 45 .12 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 5 .36 RPM |
| SRP012922_heart | 0 .00 RPM | 1 .39 RPM |
| SRP012922_kidney | 0 .00 RPM | 23 .55 RPM |
| SRP012922_liver | 0 .00 RPM | 4 .49 RPM |
| SRP012922_lung | 0 .00 RPM | 107 .52 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 0 .69 RPM |
| SRP012922_spleen | 0 .00 RPM | 78 .06 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_1735 was not experimentally validated.