RetrogeneDB ID: retro_dnov_2414

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_7284:7833..9125(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CSRP2BP
• Ensembl ID: ENSDNOG00000008372
• Aliases: None
• Description: CSRP2 binding protein [Source:HGNC Symbol;Acc:15904]

Sequence

>retro_dnov_2414
GCTGCCTCTACTTTAAAAGTAAAAGCCTCAAAACCAACTTTAGATCCCATCATTACTGTTGAGGGACTTAGGAAATGGGT
GAGCTGGAATCCTATGTAATCTGCCATGGAATTCAAAGAGAAAAGGTCTCAAACTCAGGAAGTGAAAGACATTAGAAGAG
CCCAGAAGGAAGGGGCTGGCTTTCTTGACAGGAGCACTTGTTCTATCCCCATAACATTCATAAGCCAAGGCCGCAGGCCA
GACATGATTCCTAAAAAAGGAGAAGTGATTGACTTCTCCTCCTTGAGCTCCTCCGATTGCTGGCCACTCACCAGCCCCTC
TCCTTATCCATCTCTGGACTTCTCTGCCCCTGGAACACCAGCCTCTCATTCAGCCACTCCCAACTTGCTTTCAGAAGCAG
ATCTTATTCCCAATGTGATACCACCACAAGCCTTGTTTCATGATGATGATGAGGTGGAAGGCGATGGAGTCATAGACCCT
GGGATGGAGTATGTCTCACCCCCTGCTGGTGCAGAAGCTTCTGGGACAATGGTCAGGGGCAGAAAGAAGGTCAGGGCCCC
GACCAGATAAAGCAGGAGGTGGAGAGTGAGGAGGAAAAACCCGACAGGATGGACATTGACAGTGAGGACTCAGATTCAAA
CACATCTTTGCAAGCAAGGACTCGAGAAAAGAGGAAACCTCAACTAGAGAAGGATATGAAACGTAAAGGTCCCAAGAATA
TGCCCGTGAGCATCTGAGGAAAAGCTGCTCCTGAAGAGGCTGGAAGCTTGTCCCGGTGCTGTTGCTATGACGCAGAAAGC
TCGGAGACTGAAGCATAAACTGATTGTCAGACAAGTGAAAAGAGATTGAGGATTACCACTTTTTGAGTTGGATCAGGTCG
TTAATGCTGCTCTTCTGTTGGTTGACGGGATTTATGGAGCCAAAGTTTCCAGGATTTCAGCCGGACAAGCCACATGCAGA
ACCACCTGCCAGGACTTCAGAATCCTTGACCACTACAGACTGCCTTGTCATCCAGGAAAGGATTTCGGCACCAGACCACT
AAATTTTTGAATCGTTTGATGGGATCAGAAGATATGGCTGTGGACCAAAGTATTGTCAGCACTTATACGTCTCGGATCTT
GAAACTTTATATCAGGCATGATTACGAAACAAAATCACCCAAACTACAGCTCCTGTCACAGATCCGTTCCCACTTGCACA
AGAGTGAGCCTCAGTGGATGCCTGAGCCAAATGCACATCTCAATTACCATGATGATCAGCCAAACCACATCCCAATGATA
AACTCTATGTGT

Alignment

ORF - retro_dnov_2414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.83 %
• Parental protein coverage: 55.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SASTLKVKAASKPTLDPIITVEGLRKRVSRNPVESAMELKEKRSRTQEAKDIRRAQKEAAGFLDRSTSST
          .ASTLKVKA.SKPTLDPIITVEGLRK.VS.NP..SAME.KEKRS.TQE.KDIRRAQKE.AGFLDRST.S.
Retrocopy AASTLKVKA-SKPTLDPIITVEGLRKWVSWNPM*SAMEFKEKRSQTQEVKDIRRAQKEGAGFLDRSTCSI

Parental  PVKFISRGRRPDMILEKGEVIDFSSLSSSDRTPLTSPSPSPSLDFSAPGTPASHSATPSLLSEADLIPDV
          P..FIS.GRRPDMI..KGEVIDFSSLSSSD..PLTSPSP.PSLDFSAPGTPASHSATP.LLSEADLIP.V
Retrocopy PITFISQGRRPDMIPKKGEVIDFSSLSSSDCWPLTSPSPYPSLDFSAPGTPASHSATPNLLSEADLIPNV

Parental  MPPQALFHDDDEVEGDGVIDPGMEYVPPPAGAAASGTVVGGRKKVRA-PDQIKQEVESEEEKPDRMDIDS
          .PPQALFHDDDEVEGDGVIDPGMEYV.PPAGA.ASGT.V.GRKKVRA.PDQIKQEVESEEEKPDRMDIDS
Retrocopy IPPQALFHDDDEVEGDGVIDPGMEYVSPPAGAEASGTMVRGRKKVRA<PDQIKQEVESEEEKPDRMDIDS

Parental  EDSDSNTSLQARPREKRKPQLEKDTKPKGPKYTPVSL-YEEKLLLKRLEACPSAVAMTPEARRLKRKLIV
          EDSDSNTSLQAR.REKRKPQLEKD.K.KGPK..PVS...E..LL.KRLEACP.AVAMT..ARRLK.KLIV
Retrocopy EDSDSNTSLQARTREKRKPQLEKDMKRKGPKNMPVSI>EEKLLL-KRLEACPGAVAMTQKARRLKHKLIV

Parental  RQAKRDRGLPLFDLDQVVNAALLLVDGIYGAKDGGVSRLPAGPATYRTTCQDFRILDRY-QTALPSRKGF
          RQ.KRD.GLPLF.LDQVVNAALLLVDGIYGAK...VSR..AG.AT.RTTCQDFRILD.Y.QTAL.SRKGF
Retrocopy RQVKRD*GLPLFELDQVVNAALLLVDGIYGAK---VSRISAGQATCRTTCQDFRILDHY<QTALSSRKGF

Parental  RHQTTKFLYRLVGSEDMAVDQSIVSPYTSRILKPYIRRDYETKPPKLQLLSQIRSHLHRSEPQWMPEPDA
          RHQTTKFL.RL.GSEDMAVDQSIVS.YTSRILK.YIR.DYETK.PKLQLLSQIRSHLH.SEPQWMPEP.A
Retrocopy RHQTTKFLNRLMGSEDMAVDQSIVSTYTSRILKLYIRHDYETKSPKLQLLSQIRSHLHKSEPQWMPEPNA

Parental  PLDYCYVRPNHIPTINSMC
          .L.Y....PNHIP.INSMC
Retrocopy HLNYHDDQPNHIPMINSMC

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012922_ascending_colon	0.00 RPM	51.15 RPM
SRP012922_cerebellum	0.14 RPM	42.07 RPM
SRP012922_heart	0.00 RPM	16.01 RPM
SRP012922_kidney	0.00 RPM	70.91 RPM
SRP012922_liver	0.00 RPM	21.36 RPM
SRP012922_lung	0.00 RPM	38.33 RPM
SRP012922_quadricep_muscle	0.00 RPM	39.46 RPM
SRP012922_spleen	0.00 RPM	52.65 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_2414 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005057	1 retrocopy	retro_cjac_511,
Dasypus novemcinctus	ENSDNOG00000008372	1 retrocopy	retro_dnov_2414 ,