RetrogeneDB ID: | retro_dnov_2556 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_85499:5052..6046(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ZSCAN4 | ||
| Ensembl ID: | ENSDNOG00000011483 | ||
| Aliases: | None | ||
| Description: | zinc finger and SCAN domain containing 4 [Source:HGNC Symbol;Acc:23709] |
Retrocopy-Parental alignment summary:
>retro_dnov_2556
ATGGCTTTAGATCTCAGGACCTCCTTTCAACGTGAGCCATCCAGGAATGATTGTGGATCAGAAAATATAGAGTTTGAACC
CACCCAAAGATCTGGTGTCCAGAAGGGAGAGGAGATCTTTGATTTCCAGATCACTCGGCTCAACTCATTTCAAAATGATA
ATTCATGCGTGAGGAAGGAAGTGCAAAGACTCCATAAATTTTTCCACTTGTGGCTGCAGCCTGAAAAACACACCAAGGAT
GAAATCATTTCTCAGTTGGTCCTGGAACAGTTTATGCTGAATGGACACAGCAGAAACAGGGCCTCTTTGAAGAAGAAATG
GGAGTCAAGTGGAAGAAACCTGGATAGATTCATGGAAGACGTGACTGATGACTGCATGAATCCGCCTGGCTTTGTCCATG
TTCACATGCGGGGACAGGAAGCCCTCTTCTCTGAGAATATGTCCTTAAGAGAAGTAATTATTCAGCTCAAGGGACAGTCA
TTAGCAGGAAGCTCAACAGGACAGAACAGGAGGATGCCATGCTGGTATGCCCAAGATACTCCCCTGCAAACAGAACAAGA
AGATGAACTAAAAGAAGGTGACCCAAATATTTCCGGGAAAATTACTCAAGAAATTGACAATATTATGAGTCAAAGCAATC
AAGTACCTTCCCCAATTATCACTCAGGAAGAGAACTGCAATAAGTCTGAAGAGGGAGGTATTTCTTGGGAGAACTCTGCA
TAACTCCAGAAGAACAAAGCTTGGCTCACCCAAATCCCAGGAAGGATCCCTAGAAAGACCCTCTTATCAAGATGTCCCTA
TGGAAGTGGAACCACAGTTTCTCCCCAGGCCTGACCAGGCCATACCGGAGCCTATCCCTACCCACCAGAGCAATGATGGA
ACATCCAGATGTGGGATACACCAAGAAAGAGTCCACAGTCCCCCAAAATCATACAAATGTGAGGACTGTTCCAGGATCTT
TAGGTATCCCTCTCAGCTAGAAGCCCACCAGAGA
ORF - retro_dnov_2556 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.08 % |
| Parental protein coverage: | 76.44 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MALDLRTSFRHDPSRSGHPGSHNLELEPTQGCDLQRREGNSKFQGPQLSLYQTSNGSFAKQELKRLRKVF |
| MALDLRTSF...PSR....GS.N.E.EPTQ....Q..E....FQ...L...Q..N.S....E..RL.K.F | |
| Retrocopy | MALDLRTSFQREPSRNDC-GSENIEFEPTQRSGVQKGEEIFDFQITRLNSFQNDN-SCVRKEVQRLHKFF |
| Parental | HLWLQPEKHSKEEIISQLILEQLVMNGYCRNRSILKEKWDSSGRNLEKLVGELNDDCMKSPDFVHVHMQG |
| HLWLQPEKH.K.EIISQL.LEQ...NG..RNR..LK.KW.SSGRNL........DDCM..P.FVHVHM.G | |
| Retrocopy | HLWLQPEKHTKDEIISQLVLEQFMLNGHSRNRASLKKKWESSGRNLDRFMEDVTDDCMNPPGFVHVHMRG |
| Parental | QEALFSENMPLREVIYLME-QMPAGTPRGESMRTPFQGPQNIPLQTGHGDEYKD-DSNIFVKRNQINVNI |
| QEALFSENM.LREVI.....Q..AG...G...R.P....Q..PLQT...DE.K..D.NI..K..Q...NI | |
| Retrocopy | QEALFSENMSLREVIIQLKGQSLAGSSTGQNRRMPCWYAQDTPLQTEQEDELKEGDPNISGKITQEIDNI |
| Parental | TSQGNQVPYVVIIQEDDSPKPEEGSGSWKN-LHNFRRAELGSPTSQEGSLGESSSQDVPMEVETQFLPRT |
| .SQ.NQVP...I.QE....K.EEG..SW.N.LHN.RR..LGSP.SQEGSL...S.QDVPMEVE.QFLPR. | |
| Retrocopy | MSQSNQVPSPIITQEENCNKSEEGGISWEN>LHNSRRTKLGSPKSQEGSLERPSYQDVPMEVEPQFLPRP |
| Parental | DQASPKPALTNQSSDGTSRCGINQERVHSPPKSYKCEDCPRIFRFPSQLEAHQR |
| DQA.P.P..T.QS.DGTSRCGI.QERVHSPPKSYKCEDC.RIFR.PSQLEAHQR | |
| Retrocopy | DQAIPEPIPTHQSNDGTSRCGIHQERVHSPPKSYKCEDCSRIFRYPSQLEAHQR |
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 | 0 .00 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 0 .14 RPM |
| SRP012922_heart | 0 .00 RPM | 0 .00 RPM |
| SRP012922_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP012922_liver | 0 .00 RPM | 0 .00 RPM |
| SRP012922_lung | 0 .00 RPM | 0 .00 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 0 .00 RPM |
| SRP012922_spleen | 0 .00 RPM | 0 .00 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_2556 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 5 parental genes, and 16 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000005419 | 2 retrocopies | |
| Dasypus novemcinctus | ENSDNOG00000011483 | 11 retrocopies |
retro_dnov_1048, retro_dnov_1253, retro_dnov_1287, retro_dnov_1505, retro_dnov_174, retro_dnov_1780, retro_dnov_2499, retro_dnov_2556 , retro_dnov_2666, retro_dnov_859, retro_dnov_964,
|
| Equus caballus | ENSECAG00000015200 | 1 retrocopy | |
| Loxodonta africana | ENSLAFG00000003257 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000023779 | 1 retrocopy |