RetrogeneDB ID: retro_dnov_2321

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_6400:110439..110971(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2E2
• Ensembl ID: ENSDNOG00000005031
• Aliases: None
• Description: general transcription factor IIE, polypeptide 2, beta 34kDa [Source:HGNC Symbol;Acc:4651]

Sequence

>retro_dnov_2321
AAGAAACAATGGCTAATAACTGAGGCATTGGTCAACAATCCCAAAATTGAAGCAATAGATGGGAAGTATGCCTTCGAGCC
CAAGTCCGACTTGAAAGGTAAGAAGGCTCTCCTTGGGCTCTTAGGTAAGCAGGAGTAGAGAGGCTTTGGAGGGATTCTTT
TAGAAGAAATAGAGGATGGTCTCCCCAACTAACAGAAAGCTGTCAAGGCTTTTGGGGACCAGATACTATTTGTAAACCAT
CTTGATAAGAAGAAAACTTTCTTTTCTCAATGATAAGTGCTGTCACTTTTCTGTGCATGAAGAATTTCAGAAACTTTGGA
GAAATGTCATGGTGGATTCAACGGATGAGGAGAAAATTGAAGAGAGTCTGAATTGACAGGATATTTCTTTCATCCAGGAA
TCCGGATCAAAGAAAGTGGCCCCTATTCAGAGGAAGAAAAAGCCTACTTCATAGGAAAAGTGGTGATTTAAGACTCATAA
TAAACACTTGGCTGGAATGCTGAAGTATTACTCGGACATTACTCCTGGCAAA

Alignment

ORF - retro_dnov_2321 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.47 %
• Parental protein coverage: 60.69 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QKQWLMTEALVNNPKIEVIDGKYAFKPKYNLKDKKALLRLLDKHDQRGLGGILLEDIEEGLPNSQKAVKA
          .KQWL.TEALVNNPKIE.IDGKYAF.PK..LK.KKALL.LL.K...RG.GGILLE.IE.GLPN.QKAVKA
Retrocopy KKQWLITEALVNNPKIEAIDGKYAFEPKSDLKGKKALLGLLGKQE*RGFGGILLEEIEDGLPN*QKAVKA

Parental  LGDQILFVNRPDKK-KILFFNDKSCQFSVDEEFQKLWRSVTVGSMDEEKIEEYLTRQGISSMQESRPKKV
          .GDQILFVN..DKK.K..F.NDK.C.FSV.EEFQKLWR.V.V.S.DEEKIEE.L..Q.IS..QES..KKV
Retrocopy FGDQILFVNHLDKK>KLSFLNDKCCHFSVHEEFQKLWRNVMVDSTDEEKIEESLN*QDISFIQESGSKKV

Parental  APIQRKKKPASQNKLRFKTHNEHLAGVLD-YSEIAPGK
          APIQRKKKP.S..K..FKTHN.HLAG.L..YS.I.PGK
Retrocopy APIQRKKKPTS*EKW*FKTHNKHLAGMLKYYSDITPGK

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	8.95 RPM
SRP012922_cerebellum	0.00 RPM	15.12 RPM
SRP012922_heart	0.00 RPM	7.43 RPM
SRP012922_kidney	0.00 RPM	9.04 RPM
SRP012922_liver	0.00 RPM	5.73 RPM
SRP012922_lung	0.00 RPM	11.91 RPM
SRP012922_quadricep_muscle	0.00 RPM	7.10 RPM
SRP012922_spleen	0.00 RPM	14.19 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_2321 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000005031	1 retrocopy	retro_dnov_2321 ,
Macropus eugenii	ENSMEUG00000010541	1 retrocopy	retro_meug_546,
Myotis lucifugus	ENSMLUG00000007814	1 retrocopy	retro_mluc_2029,
Sorex araneus	ENSSARG00000007758	2 retrocopies	retro_sara_376, retro_sara_569,
Sus scrofa	ENSSSCG00000015845	1 retrocopy	retro_sscr_878,
Tarsius syrichta	ENSTSYG00000013143	1 retrocopy	retro_tsyr_2074,
Tursiops truncatus	ENSTTRG00000012464	1 retrocopy	retro_ttru_859,