RetrogeneDB ID: retro_dnov_2192

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_54290:352..1135(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35B1
• Ensembl ID: ENSDNOG00000009256
• Aliases: None
• Description: solute carrier family 35, member B1 [Source:HGNC Symbol;Acc:20798]

Sequence

>retro_dnov_2192
TTAACTCTGGTCTTCATCCAATGTGTGATCAATGCTGTTTGCCAAGATCCGGTGGATCGTACCCGGAGCTGGCTCAATGC
TGCTTGTTCTATCTCCTGTCTGGGTGTCATGGTCTCCAGCAACTCAGCACTGCAGTTTATCAACTACCCATCCCAGGTCC
TTGGTAAATCCTGCAAGCCAATCCCAGTCATGCTCCTTGGCCTAACTCTTCTGAAGAAAAAGTACCCACTGGTCAAGTAC
CTGTGCGTGTTACTTTTTGTGGCTGGAGTTGCTCTTGCCATGTACAAACCCAAGAAAGTGATTGGAATGGAAGAACACAC
AGCTGGCTACGGAGAGCTGCTCCTGCTGTTGTCTCTGACCCTGGATGGACTGACAGGTGTTTCCCAGGACCACATGCGGG
CTCATTACCGAACAGACTCCAAACACATGATGTTGAATATCAACCTTTGGTCAACGTTGCTGCTGAGAGCCGGAATCCTG
TTCACTGGACAGCTCTGGGAGTTCTTGAGCTTTGCTGAGAGATACCCTGCCATCATCTATAACATCCTGCTCTTCGGCCT
GACCCGTGCCCTGGGTCAGAGCTGCATCTTCATGACAGTTGTGTATTTTGGCCCCTTGACCTGTTCAGTCATCACCACGA
CTCAGAAGTTCTTCATCATCTTGGCCTCTGTGATCCTCTTTGCCAGCCCCATCAGCCCCGTGCAGTGGGTAGGCACTGTG
CTTGTGTTCCTGGGTCTCAGCCTTGATGCCAAATTTGGGAAAGGTGCCAAGAAGACATCCCAC

Alignment

ORF - retro_dnov_2192 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.44 %
• Parental protein coverage: 81.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  INAVFAKILIQFFDTARVDRTRSWLYAACSISYLGAMVSSNSALQFVNYPTQVLGKSCKPIPVMLLGVTL
          ...VF....I.......VDRTRSWL.AACSIS.LG.MVSSNSALQF.NYP.QVLGKSCKPIPVMLLG.TL
Retrocopy LTLVFIQCVINAVCQDPVDRTRSWLNAACSISCLGVMVSSNSALQFINYPSQVLGKSCKPIPVMLLGLTL

Parental  LKKKYPLAKYLCVLLIVAGVALFMYKPKKVVGMEEHTVGYGELLLLLSLTLDGLTGVSQDHMRAHYQTGS
          LKKKYPL.KYLCVLL.VAGVAL.MYKPKKV.GMEEHT.GYGELLLLLSLTLDGLTGVSQDHMRAHY.T.S
Retrocopy LKKKYPLVKYLCVLLFVAGVALAMYKPKKVIGMEEHTAGYGELLLLLSLTLDGLTGVSQDHMRAHYRTDS

Parental  NHMMLNINLWSTLLLGAGILFTGELWEFLSFAERYPAIIYNILLFGLTSALGQSFIFMTVVYFGPLTCSI
          .HMMLNINLWSTLLL.AGILFTG.LWEFLSFAERYPAIIYNILLFGLT.ALGQS.IFMTVVYFGPLTCS.
Retrocopy KHMMLNINLWSTLLLRAGILFTGQLWEFLSFAERYPAIIYNILLFGLTRALGQSCIFMTVVYFGPLTCSV

Parental  ITTTRKFFTILASVILFANPISPMQWVGTVLVFLGLGLDAKFGKGAKKTSH
          ITTT.KFF.ILASVILFA.PISP.QWVGTVLVFLGL.LDAKFGKGAKKTSH
Retrocopy ITTTQKFFIILASVILFASPISPVQWVGTVLVFLGLSLDAKFGKGAKKTSH

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	91.79 RPM
SRP012922_cerebellum	0.00 RPM	61.17 RPM
SRP012922_heart	0.00 RPM	46.64 RPM
SRP012922_kidney	0.00 RPM	77.76 RPM
SRP012922_liver	0.00 RPM	50.93 RPM
SRP012922_lung	0.00 RPM	62.16 RPM
SRP012922_quadricep_muscle	0.00 RPM	102.99 RPM
SRP012922_spleen	0.00 RPM	77.15 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_2192 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009256	2 retrocopies	retro_dnov_1341, retro_dnov_2192 ,
Echinops telfairi	ENSETEG00000014331	2 retrocopies	retro_etel_1033, retro_etel_1819,