RetrogeneDB ID: retro_dnov_989

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_131277:34..511(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD23B
• Ensembl ID: ENSDNOG00000001174
• Aliases: None
• Description: RAD23 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:9813]

Sequence

>retro_dnov_989
GAGACACCAGTGGCTGCCTGCCCAACATGAACTGACAGCACATCAGGAGATTCTTCTTGGCCAAATCTTATTGAAGATGC
AACAAGTACACTTGTGACAGGCAGTCTTATGAGACTATGGTAACTGAGTTCATGTCTACCGGCTATGAAAGAAAGTAAGT
AATTGCAGCTCAGAGAGCCAGTTTCAACAACCCTGACAGAGCAGTGAAGTACCTTTTAATGGGAATCCCTGGAGACAGAG
AAAGTCAGGCTGTGGTGGACCCTCCTCAAGCAGCGAGTACTGGGGCTCCTCAGTCCGCAAAGTAGCTGCAATTGCAACAA
CTATGACCGCAACAACTGCAATAGCAAGTTTTGGAGGACATCAGCTTGAAGTTTTACAAAATCAGCCTCCATTCCAACAG
ATGAGACAAATCGTCAACAGAATCCTTCCCTGCTTCCAGCACTGCTACAGATAGGTCGAGAGAATCCCCGTTTACTG

Alignment

ORF - retro_dnov_989 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.49 %
• Parental protein coverage: 51.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ETPVATSPTSTDSTSGDSSRSNLFEDATSALVTG-QSYENMVTEIMSMGYEREQVIAALRASFNNPDRAV
          ETPVA..PT.TDSTSGDSS..NL.EDATS.LVTG.QSYE.MVTE.MS.GYER..VIAA.RASFNNPDRAV
Retrocopy ETPVAACPT*TDSTSGDSSWPNLIEDATSTLVTG<QSYETMVTEFMSTGYERK*VIAAQRASFNNPDRAV

Parental  EYLLMGIPGDRESQAVVDPPQAASTGAPQSS-AVAAAAATTTATTTTASSGGHPLEFLRNQPQFQQMRQI
          .YLLMGIPGDRESQAVVDPPQAASTGAPQS...VAA.A.T.TATT..AS.GGH.LE.L.NQP.FQQMRQI
Retrocopy KYLLMGIPGDRESQAVVDPPQAASTGAPQSA<KVAAIATTMTATTAIASFGGHQLEVLQNQPPFQQMRQI

Parental  I-QQNPSLLPALLQQIGRENPQLL
          ..QQNPSLLPALL.QIGRENP.LL
Retrocopy V<QQNPSLLPALL-QIGRENPRLL

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	79.93 RPM
SRP012922_cerebellum	0.00 RPM	58.42 RPM
SRP012922_heart	0.00 RPM	21.35 RPM
SRP012922_kidney	0.00 RPM	22.73 RPM
SRP012922_liver	0.00 RPM	37.00 RPM
SRP012922_lung	0.00 RPM	38.79 RPM
SRP012922_quadricep_muscle	0.00 RPM	79.79 RPM
SRP012922_spleen	0.00 RPM	41.89 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_989 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001926	1 retrocopy	retro_btau_877,
Callithrix jacchus	ENSCJAG00000016908	2 retrocopies	retro_cjac_3865, retro_cjac_4184,
Dasypus novemcinctus	ENSDNOG00000001174	2 retrocopies	retro_dnov_1982, retro_dnov_989 ,
Equus caballus	ENSECAG00000021928	1 retrocopy	retro_ecab_361,
Loxodonta africana	ENSLAFG00000007533	1 retrocopy	retro_lafr_1109,
Oryctolagus cuniculus	ENSOCUG00000007316	1 retrocopy	retro_ocun_1429,
Sarcophilus harrisii	ENSSHAG00000011925	1 retrocopy	retro_shar_248,
Sus scrofa	ENSSSCG00000005436	1 retrocopy	retro_sscr_770,
Tursiops truncatus	ENSTTRG00000007597	1 retrocopy	retro_ttru_1401,