RetrogeneDB ID: retro_dnov_43

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_74747:5903..7250(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000016491
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TUBA1A
• Ensembl ID: ENSDNOG00000004121
• Aliases: None
• Description: tubulin, alpha 1a [Source:HGNC Symbol;Acc:20766]

Sequence

>retro_dnov_43
CGTGAGTGCATCTCCATCCACGTCGGCCAGGCTGGTGTCCAGATTGGCAATGCCTGCTGGGAGCTCTACTGCCTGGAACA
CGGCATCCAGCCCGATGGCCAGATGCCAAGTGACAAGACCATTGGGGGAGGAGATGACTCCTTCAACACCTTCTTCAGTG
AGACTGGCGCTGGCAAGCATGTGCCCAGGGCAGTGTTTGTAGACCTGGAACCCACAGTCATTGATGAAGTTCGCACTGGC
ACCTACCGCCAGCTCTTCCACCCTGAGCAGCTCATCACAGGCAAGGAAGATGCTGCCAATAACTATGCCCGTGGGCATTA
CACCATCGGCAAGGAGATCATCGACCTGGTTCTGGACAGAATTCGCAAACTGGCCGACCAGTGCACAGGGCTTCAGGGCT
TCTTGGTTTTCCACAGCTTTGGTGGGGGAACGGGTTCCGGGTTCACCTCCCTGCTGATGGAACGCCTTTCTGTTGATTAC
GGCAAGAAGTCCAAGCTGGAGTTCTCCATTTACCCAGCCCCCCAGGTCTCCACAGCTGTGGTCGAGCCCTACAACTCCAT
CCTCACCACCCACACCACCCTGGAGCACTCAGATTGTGCCTTCATGGTAGACAATGAGGCCATCTATGACATCTGTCGCA
GAAATCTTGATATTGAGCGCCCAACCTACACCAACCTTAACCACCTTATTAGCCAGATTGTGTCCTCCATCACAGCCTCC
CTCAGGTTTGATGGTGCCCTGAATGTAGATCTGACAGAATTCCAGACCAACCTGGTGCCCTATCCCCGCATCCACTTTCC
TCTGGCCACATCCGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAGCAGCTTTCTGTAGCAGAGATTACCAATGCTT
GCTTTGAGCCGGCCAACCAGATGGTGAAATGCGACCCTAACCACGGTAAATACATGGCCTGCTGCCTGTTGTACCGGGGC
GACGTGGTTCCCAAAGACGTCAATGCTGCCATTGCCACCATCAAGACCAAGCGCACCATCCAGTTTGTGGACTGGTGTCC
CACTGGCTTCAAGGTCAGCATTAATTACCAGCCTCCCACTGTGGTTCCTGGTGGCGACCTGGCCAAGGTCCAGCGAGCTG
TGTGCATGCTGAGCAACACCACAGCCGTGGCCGAGGCCTGGGCTCGCCTGGACCACAAGTTTGACCTGATGTACGCCAAG
CGTGCCTTTGTCCACTGGTACGTGGGGGAGGGAATGGAGGAAGGAGAGTTCTCTGAGGCCCGTGAGGACATGGCTGCCCT
CGAGAAGGATTATGAGGAGGTTGGGGCAGATAGTGGCGAGGGAGAGAATGAGGGTGAGGAGTATTAG

Alignment

ORF - retro_dnov_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.0 %
• Parental protein coverage: 99.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLE
          RECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLE
Retrocopy RECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLE

Parental  PTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSF
          PTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSF
Retrocopy PTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSF

Parental  GGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYD
          GGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYD
Retrocopy GGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYD

Parental  ICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDQTEFPTKLVPYPHIHFPLATYAPIISVEKA
          ICRRNLDIERPTYTNLN.LI.QIVSSITASLRFDGALNVD.TEF.T.LVPYP.IHFPLAT.AP.IS.EKA
Retrocopy ICRRNLDIERPTYTNLNHLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATSAPVISAEKA

Parental  YHEQLSVAEITSVCFELANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGF
          YHEQLSVAEIT..CFE.ANQMVKCDP.HGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGF
Retrocopy YHEQLSVAEITNACFEPANQMVKCDPNHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGF

Parental  KVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKHAFVHCYMREGMEEGEFSEA
          KV.INYQPPTVVPGGDLAKVQRAVCMLSNTTA.AEAWARLDHKFDLMYAK.AFVH.Y..EGMEEGEFSEA
Retrocopy KVSINYQPPTVVPGGDLAKVQRAVCMLSNTTAVAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEA

Parental  HENMAALKKDYEEVGVDSVEGEGEEEGEDY
          .E.MAAL.KDYEEVG.DS..GEGE.EGE.Y
Retrocopy REDMAALEKDYEEVGADS--GEGENEGEEY

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	11.67 RPM	26.64 RPM
SRP012922_cerebellum	19.52 RPM	155.89 RPM
SRP012922_heart	4.41 RPM	18.56 RPM
SRP012922_kidney	9.86 RPM	14.51 RPM
SRP012922_liver	2.94 RPM	6.50 RPM
SRP012922_lung	7.18 RPM	53.00 RPM
SRP012922_quadricep_muscle	3.63 RPM	11.94 RPM
SRP012922_spleen	12.71 RPM	47.27 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_43 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 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001489	3 retrocopies	retro_btau_251, retro_btau_350, retro_btau_929,
Callithrix jacchus	ENSCJAG00000020894	2 retrocopies	retro_cjac_1209, retro_cjac_3157,
Dasypus novemcinctus	ENSDNOG00000004121	1 retrocopy	retro_dnov_43 ,
Equus caballus	ENSECAG00000013798	1 retrocopy	retro_ecab_223,
Homo sapiens	ENSG00000167552	1 retrocopy	retro_hsap_3313,
Nomascus leucogenys	ENSNLEG00000017836	2 retrocopies	retro_nleu_245, retro_nleu_2757,
Oryctolagus cuniculus	ENSOCUG00000027812	1 retrocopy	retro_ocun_197,
Pteropus vampyrus	ENSPVAG00000004645	2 retrocopies	retro_pvam_1283, retro_pvam_414,
Rattus norvegicus	ENSRNOG00000004559	3 retrocopies	retro_rnor_1200, retro_rnor_2006, retro_rnor_446,
Vicugna pacos	ENSVPAG00000005749	4 retrocopies	retro_vpac_157, retro_vpac_210, retro_vpac_429, retro_vpac_72,