RetrogeneDB ID: retro_dnov_493

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5271:40978..41446(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LGALSL
• Ensembl ID: ENSDNOG00000015222
• Aliases: None
• Description: lectin, galactoside-binding-like [Source:HGNC Symbol;Acc:25012]

Sequence

>retro_dnov_493
AAACAAGAGGAAGGGCATTTAAACAACTCCTTGGGGTCTACAGTTCAAGTAGACTTGTACTTCCCATGACTGACAGTTCC
ATTTTGTGGGCACATTAAAGGTGGCATGAAACCAGGCAAAAAGGTATTATTAGTGGGGGCATCATAGACCTTAACCCAGA
TAGCTTGACCTGTGGTAACTCAGAAGATCCTCCAGCGGATGTGATGACTGAACTCAAAGCTGTGTTCATAGACCTGCAGG
TACTCAGGAATTCCTGCATATCTGGGGGATAGTGTGAAGAACAGTCAGCAATCCTTAACTTTCCATTCATCCCAGACCAA
CCATTCCGACTGGAAATTCTTTGTGAGCAGCCATGATTGGGAGTGTTTGTGGATGGATACCAACTTTTTAATTTTTTGCC
ACCACTTTCAAATGTTACCTGCAATCAACATCAAAAAAATAAATGGGGACCTCCAGATCACTAAGCTC

Alignment

ORF - retro_dnov_493 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.43 %
• Parental protein coverage: 99.38 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KLDDGHLNNSLGSPVQADLYFPRLIVP-FCGHIKGGMKPGKK-VLVMGIVDLNPESFAISLTCGDSEDPP
          K...GHLNNSLGS.VQ.DLYFP.L.VP.F.G..K......K......GI.DLNP.....SLTCG.SEDPP
Retrocopy KQEEGHLNNSLGSTVQVDLYFP*LTVP>FVGTLKVA*NQAKR>IISGGIIDLNPD----SLTCGNSEDPP

Parental  ADVAIELKAVFTDRQLLRNSCISGERGEEQSAIPYFPFIPDQPFRVEILCEHPRFRVFVDGHQLFDFY-H
          ADV..ELKAVF.D.Q.LRNSCISG...EEQSAI..FPFIPDQPFR.EILCE.P...VFVDG.QLF.F..H
Retrocopy ADVMTELKAVFIDLQVLRNSCISGG*CEEQSAILNFPFIPDQPFRLEILCEQP*LGVFVDGYQLFNFL>H

Parental  RIQTLSAIDTIKINGDLQITKL
          ..Q.L.AI...KINGDLQITKL
Retrocopy HFQMLPAINIKKINGDLQITKL

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	9.72 RPM
SRP012922_cerebellum	0.00 RPM	9.49 RPM
SRP012922_heart	0.00 RPM	4.64 RPM
SRP012922_kidney	0.00 RPM	8.21 RPM
SRP012922_liver	0.00 RPM	6.81 RPM
SRP012922_lung	0.15 RPM	5.65 RPM
SRP012922_quadricep_muscle	0.00 RPM	51.93 RPM
SRP012922_spleen	0.00 RPM	15.22 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_493 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001067	1 retrocopy	retro_amel_429,
Bos taurus	ENSBTAG00000000156	1 retrocopy	retro_btau_1263,
Dasypus novemcinctus	ENSDNOG00000015222	1 retrocopy	retro_dnov_493 ,
Felis catus	ENSFCAG00000001209	1 retrocopy	retro_fcat_1280,
Monodelphis domestica	ENSMODG00000003226	2 retrocopies	retro_mdom_1350, retro_mdom_233,
Mus musculus	ENSMUSG00000042363	3 retrocopies	retro_mmus_1637, retro_mmus_272, retro_mmus_2942,
Sarcophilus harrisii	ENSSHAG00000011885	2 retrocopies	retro_shar_315, retro_shar_732,