RetrogeneDB ID: retro_dnov_2085

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_465:103258..103958(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIX1
• Ensembl ID: ENSDNOG00000012335
• Aliases: None
• Description: Lix1 homolog (chicken) [Source:HGNC Symbol;Acc:18581]

Sequence

>retro_dnov_2085
GTGAGTGTGGTGGAGGCGCTGCAGCAGTTCTGGCAGATGAAGCAGTCCCTTGGGGCTGACTTGAAGAATGGGGCTTTAGC
GGTTTTGAGATGGTGCCTACCAACAGCCCTCTCTATGTCTGCTATGTCACCCTGCCGGGGGGAAGTTGCTTTGGGAGTTT
CCAGGTTTGTCCCACAAAAGCTGAGGCTCGGCGGAGTGCTGCAAAGATTGCACTAATGAACTCTGTGTTTAATGCACATC
CTTCCCGGAGAATCACTGATGAGTTCATTGAGAAGAGTGTCTCTGAGCCTTTGGCATCTTTCAGCGGCAACAGGGAGGAG
GCTGACAACCCAAATACAGGGACTGGTGCCTTCGGATTCATGTTGGAACCCAACAAGGGCAAGTCAGTGTTGGAGTTCCA
GGAGTTAATGACAGTTTTTCAACTGCTGCACTGGAATGGCAGCCTTCAGGCCATGAGGGAAAGACCGAGCTCTCAGCAAG
AGGTGCTGGCTCATTATTCACCCCCAGCCCTGGATGATGATATTCGCCACCAAATGGCATTGCACTGGGTGAGCCGGGAG
AGAGTGTGCCAGGGGCACTGTCTAGAGAGCTGGCCTCCACTGAGTGGGAGCTGGATGAAGCCTGGCTGGGAGGCAAGTTG
CTGTGCTTCCACAAGGAGAAGAAAGATATTCTCATGCTGGCTGCTGGGCAGTTGGGCAAC

Alignment

ORF - retro_dnov_2085 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.27 %
• Parental protein coverage: 82.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LNVVSMLQEFWESKQQQRAAFPSEGIVV-YESLPSPGPPFVSYVTLPGGSCFGNFQCCLSRAEARRDAAK
          ..VV..LQ.FW..KQ...A........V..E..P...P..V.YVTLPGGSCFG.FQ.C...AEARR.AAK
Retrocopy VSVVEALQQFWQMKQSLGADLKNGALAV<FEMVPTNSPLYVCYVTLPGGSCFGSFQVCPTKAEARRSAAK

Parental  VALINSLFNELPSRRITKEFIMESVQEAVASTSGTLDDADDPSTSIGAYHYMLESNMGKTMLEFQELMTI
          .AL.NS.FN..PSRRIT.EFI..SV.E..AS.SG....AD.P.T..GA...MLE.N.GK..LEFQELMT.
Retrocopy IALMNSVFNAHPSRRITDEFIEKSVSEPLASFSGNREEADNPNTGTGAFGFMLEPNKGKSVLEFQELMTV

Parental  FQLLHWNGSLKALRETKCSRQXXXXXXXXXXXXXXXXXXMALDWIMKR-ES-PGILSQELRMVLRELEEA
          FQLLHWNGSL.A.RE...S.Q..................MAL.W.....ES.PG.LS.EL.....EL.EA
Retrocopy FQLLHWNGSLQAMRERPSSQQEVLAHYSPPALDDDIRHQMALHWVSRE<ESVPGALSRELASTEWELDEA

Parental  RKAGQELRFYKEKKEIVSLALTQIYN
          ...G..L.F.KEKK.I..LA..Q..N
Retrocopy WLGGKLLCFHKEKKDILMLAAGQLGN

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	1.17 RPM	0.78 RPM
SRP012922_cerebellum	1.37 RPM	1.92 RPM
SRP012922_heart	2.09 RPM	0.00 RPM
SRP012922_kidney	0.82 RPM	0.00 RPM
SRP012922_liver	2.01 RPM	0.00 RPM
SRP012922_lung	3.82 RPM	0.00 RPM
SRP012922_quadricep_muscle	0.69 RPM	0.17 RPM
SRP012922_spleen	4.92 RPM	0.00 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_2085 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012335	1 retrocopy	retro_dnov_2085 ,
Equus caballus	ENSECAG00000021643	1 retrocopy	retro_ecab_1013,
Mus musculus	ENSMUSG00000047786	1 retrocopy	retro_mmus_448,