RetrogeneDB ID: retro_dnov_2261

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_59675:9706..10275(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RANGRF
• Ensembl ID: ENSDNOG00000018164
• Aliases: None
• Description: RAN guanine nucleotide release factor [Source:HGNC Symbol;Acc:17679]

Sequence

>retro_dnov_2261
ATGAAGCCCACAAGAGACTATCCACTGCTCAGAGATGCGTTCTCCGCCAAGCTCCCGGTTGGGGCCAGTGATATAAGCGA
CCACCGACCAGTCCTGGACAATCAAGAAGTTTTCTGCCATCACGCAACCGACCAGAGCCTGATCGTGGAACTTCTGGAGC
TGCAGGTCTACATGCAGGGCCGAGAGGCTGCATGGTACCACTTTGAGGATGCTGGTGGGGTGCAGGGTGCTAGGACTGTG
CAAGTGGAAGCTGTGCAGCCTCTCCCGGTGGACAGCCTAACCCTGAGGGGCTGCTGTCAAGAAGCCTGGATCCTCTCTGG
AAAGTAGCAAGTGGCTAAGGAAAACCAGCAGGTAGCAAAGGAGGTGACACTGCACCAGGCCTTGCTGCAGCTGCCCAGTA
CCAAACTGATCTGCTCACCTTCAGTCAGCCCCCTTCCCCCATAGCAAGCCCTGAGATCAGGTCATCTCTCAGCTCTGAAA
ATCTGTCACCCCTGCCATGGAGCCTGGATGACTTTGAGCAGCTGGTGACCAGCCTGACCCTTCATGATCCCAACATCTTT
GGTCCCCAA

Alignment

ORF - retro_dnov_2261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEPTRGYPLFGGAFSAKLPVGAIDVSDLRPVPDNQEVFCHRATDQSLIVELLELQVHVQGREAARYHFED
          M.PTR.YPL...AFSAKLPVGA.D.SD.RPV.DNQEVFCH.ATDQSLIVELLELQV..QGREAA.YHFED
Retrocopy MKPTRDYPLLRDAFSAKLPVGASDISDHRPVLDNQEVFCHHATDQSLIVELLELQVYMQGREAAWYHFED

Parental  VGGVQGARTVQVEAVQPLPVESLALRGCCQEAWILSGKQHVAKENQQVAKEVTLHQALLRLP-QYQTDLL
          .GGVQGARTVQVEAVQPLPV.SL.LRGCCQEAWILSGK..VAKENQQVAKEVTLHQALL.LP.QYQTDLL
Retrocopy AGGVQGARTVQVEAVQPLPVDSLTLRGCCQEAWILSGK*QVAKENQQVAKEVTLHQALLQLP<QYQTDLL

Parental  LTFSQPP----PEIRSSLGPESLSPLPWSLDDFEQLVTSLTLHDPNIFGPQ
          .....P.....PEIRSSL..E.LSPLPWSLDDFEQLVTSLTLHDPNIFGPQ
Retrocopy TFSQPPSPIASPEIRSSLSSENLSPLPWSLDDFEQLVTSLTLHDPNIFGPQ

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	0.39 RPM	28.39 RPM
SRP012922_cerebellum	0.00 RPM	12.10 RPM
SRP012922_heart	0.00 RPM	20.19 RPM
SRP012922_kidney	0.27 RPM	23.00 RPM
SRP012922_liver	1.39 RPM	9.75 RPM
SRP012922_lung	0.92 RPM	19.55 RPM
SRP012922_quadricep_muscle	0.17 RPM	23.19 RPM
SRP012922_spleen	0.34 RPM	33.42 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_2261 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012555	1 retrocopy	retro_chof_14,
Dasypus novemcinctus	ENSDNOG00000018164	1 retrocopy	retro_dnov_2261 ,
Dipodomys ordii	ENSDORG00000007147	2 retrocopies	retro_dord_325, retro_dord_346,
Macropus eugenii	ENSMEUG00000006399	2 retrocopies	retro_meug_1091, retro_meug_220,
Mus musculus	ENSMUSG00000032892	2 retrocopies	retro_mmus_175, retro_mmus_2983,
Rattus norvegicus	ENSRNOG00000004980	4 retrocopies	retro_rnor_1148, retro_rnor_2982, retro_rnor_2983, retro_rnor_759,