RetrogeneDB ID: | retro_dnov_815 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_10989:78196..79120(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CNN3 | ||
| Ensembl ID: | ENSDNOG00000012883 | ||
| Aliases: | None | ||
| Description: | calponin 3, acidic [Source:HGNC Symbol;Acc:2157] |
Retrocopy-Parental alignment summary:
>retro_dnov_815
GCCAGCATGAGCTCCTCGCAGTTCAACAAGGGCCCCTCGTACGGGCTCTCGGCCGAGGTCAAGAACCGGCTCCTGTCCAA
ATATGACCCTCAGAAGGAGGCAGAGCTCCGCAGCTGGATCGAGGGGCTCACGGGACTTTCTATTGGCCCCGACTTCCAGA
AAGGCCTGAAGGATGGAGTTATCTTGTGCACGCTCATGAACAAGCTGCAGCCGGGCTCCGTCCCCAAGGTCAACCGCTCC
CAGCAGAACTGGCACCAGCTGGAGAACCTGTCCAACTTCATCAAGGCCATGGTCGGCTACGGCATGAACCCCGTGGACCT
GTTCGAAGCCAACGACCTCTTCGAGAGCGGGAACCTGACGCAGGTGCAGGTGTCCCTCCTCGCCCTGGCCGGGAAGGCCA
AGACGAAGGGGCTGCAGAGCGGCGTGGACATCGGCGTCAAGTACTCTGAGAAGCAAGAGCGCAACTTCGACGACGCCACC
ATGAAGGCGGGCCAGTGCGTCATCGGGCTGCAGATGGGCACTAACAAGTGCGCCAGCCAGTCGGGCATGACGGCGTATGG
CACGCGGCGGCACCTGTACGACCCCAAGAACCACATCCTGCCGCCCATGGACCACTCCACCATCAGTCTCCAGATGGGCA
CCAACAAGTGTGCCAGCCAGGTGGGCATGACGGCTCCGGGGACCCGGCGGCACATTTACGACACCAAGCTGGGCACCGAC
AAGTGCGACAACTCTTCCATGTTCCTGCAGATGGGCTACGCGCAGGGAGCCAACCAGAGCGGCCAGGTCTTTGGCCTGGG
CCGCCAGATCTATGACCCCAAGTACTGCCCACAGGGCCCGGGGGCCGATGGGGCGCCCTCAGGCGCCGGCGACTGCCCGG
ACGCCCCCGAGGCCCCCGAGTATGCTCCCTACTACCAGGAGGAG
ORF - retro_dnov_815 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 60.13 % |
| Parental protein coverage: | 77.39 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ARATMTHFNKGPSYGLSAEVKNKIASKYDHQAEEDLRSWIEEVTGMSIGTNFQLGLKDGIILCELINKLQ |
| A......FNKGPSYGLSAEVKN...SKYD.Q.E..LRSWIE..TG.SIG..FQ.GLKDG.ILC.L.NKLQ | |
| Retrocopy | ASMSSSQFNKGPSYGLSAEVKNRLLSKYDPQKEAELRSWIEGLTGLSIGPDFQKGLKDGVILCTLMNKLQ |
| Parental | PGSVKKVNESSLNWPQLENIGNFIKAIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAKTKGFHT |
| PGSV.KVN.S..NW.QLEN..NFIKA...YGM.P.D.FEANDLFE.GN.TQVQ..L.ALAG.AKTKG... | |
| Retrocopy | PGSVPKVNRSQQNWHQLENLSNFIKAMVGYGMNPVDLFEANDLFESGNLTQVQVSLLALAGKAKTKGLQS |
| Parental | -IDIG-EYAEKQ-RRFDXXXXXXXXXXXXXXMGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISL |
| ..DIG..Y.EKQ.R.FD..............MGTNKCASQ.GMTAYGTRRHLYDPK.....P.D..TISL | |
| Retrocopy | GVDIGVKYSEKQERNFDDATMKAGQCVIGLQMGTNKCASQSGMTAYGTRRHLYDPKNHILPPMDHSTISL |
| Parental | QMGTNKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMGTNKVASQKGMSVYGLGRQVYDPKYCAAP |
| QMGTNK.ASQ.GM.APGTRR.IYD.KL.....DNS...LQMG....A.Q.G..V.GLGRQ.YDPKYC..P | |
| Retrocopy | QMGTNKCASQVGMTAPGTRRHIYDTKLGTDKCDNSSMFLQMGYAQGANQSG-QVFGLGRQIYDPKYC--P |
| Parental | TEPVIHNGSQGTGTNGSEISDSDYQAEYPDE |
| ..P.......G.G..........Y...Y..E | |
| Retrocopy | QGPGADGAPSGAGDCPDAPEAPEYAPYYQEE |
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 | 38 .12 RPM | 140 .99 RPM |
| SRP012922_cerebellum | 7 .01 RPM | 78 .22 RPM |
| SRP012922_heart | 16 .47 RPM | 30 .16 RPM |
| SRP012922_kidney | 25 .46 RPM | 133 .06 RPM |
| SRP012922_liver | 18 .89 RPM | 72 .45 RPM |
| SRP012922_lung | 134 .70 RPM | 197 .47 RPM |
| SRP012922_quadricep_muscle | 4 .67 RPM | 22 .67 RPM |
| SRP012922_spleen | 226 .29 RPM | 171 .23 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_815 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 6 parental genes, and 11 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000018128 | 3 retrocopies | |
| Dasypus novemcinctus | ENSDNOG00000012883 | 3 retrocopies |
retro_dnov_223, retro_dnov_403, retro_dnov_815 ,
|
| Macropus eugenii | ENSMEUG00000002921 | 2 retrocopies | |
| Monodelphis domestica | ENSMODG00000004326 | 1 retrocopy | |
| Mustela putorius furo | ENSMPUG00000003332 | 1 retrocopy | |
| Sarcophilus harrisii | ENSSHAG00000002670 | 1 retrocopy |