RetrogeneDB ID: retro_dnov_1463

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_20850:19893..20256(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM3
• Ensembl ID: ENSDNOG00000010420
• Aliases: None
• Description: RNA binding motif (RNP1, RRM) protein 3 [Source:HGNC Symbol;Acc:9900]

Sequence

>retro_dnov_1463
GTCATCGTCAAGGACCGGGAGACTCAGCGGTCTAGGGGTTTTGGCTTCATCACCTTCACCAACCCAGAGCATGCCTCAGA
TGCCATGCAGGCCATGAATGGAGAGTCCCTGGATGGGCGCCAGATCCGTGTGGACCTTGCAGGCAAGTCAGCCAGGGGAA
CCAGAAGGGGTGCCTTTGGGGGTCATGGGCGTGGTCGCAGCTACTCTAGAGGTGGTGGGAACCAAGGATATGGGAGCAGC
TGGTATGACAGTCGGCCTGGAGGATATGGATATGGATATGGCAGGTCCAGAGACTATGGTGGCAGAAACCAGGGTGGTTA
TGACCGCTACTCTGGAGGAAATTACAGAGACAATTATGACAAC

Alignment

ORF - retro_dnov_1463 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.43 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVVKDRETQRSRG-GFITFTNPEHASDAMQAM-GESLDGRQIRVDHAGKSARGTRGGAFGGHGRGRSYSR
          V.VKDRETQRSRG.GFITFTNPEHASDAMQAM.GESLDGRQIRVD.AGKSARGTR.GAFGGHGRGRSYSR
Retrocopy VIVKDRETQRSRGFGFITFTNPEHASDAMQAMNGESLDGRQIRVDLAGKSARGTRRGAFGGHGRGRSYSR

Parental  GGGDQGYGSSRYDSRPGGYGYGYGRSRDYGGRNQGGYDRYSGGNYRDNYDN
          GGG.QGYGSS.YDSRPG.......RSRDYGGRNQGGYDRYSGGNYRDNYDN
Retrocopy GGGNQGYGSSWYDSRPGXXXXXXXRSRDYGGRNQGGYDRYSGGNYRDNYDN

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	15.75 RPM	56.40 RPM
SRP012922_cerebellum	11.41 RPM	29.42 RPM
SRP012922_heart	6.96 RPM	22.28 RPM
SRP012922_kidney	8.21 RPM	38.06 RPM
SRP012922_liver	4.80 RPM	23.53 RPM
SRP012922_lung	10.39 RPM	50.86 RPM
SRP012922_quadricep_muscle	6.75 RPM	14.02 RPM
SRP012922_spleen	22.89 RPM	71.19 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_1463 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 11 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013718	1 retrocopy	retro_acar_197,
Bos taurus	ENSBTAG00000025848	1 retrocopy	retro_btau_1144,
Canis familiaris	ENSCAFG00000015485	2 retrocopies	retro_cfam_1475, retro_cfam_259,
Cavia porcellus	ENSCPOG00000003553	1 retrocopy	retro_cpor_950,
Dasypus novemcinctus	ENSDNOG00000010420	16 retrocopies	retro_dnov_1343, retro_dnov_1380, retro_dnov_1463 , retro_dnov_151, retro_dnov_1718, retro_dnov_180, retro_dnov_2034, retro_dnov_2076, retro_dnov_212, retro_dnov_213, retro_dnov_2217, retro_dnov_2367, retro_dnov_2581, retro_dnov_733, retro_dnov_778, retro_dnov_974,
Dasypus novemcinctus	ENSDNOG00000017199	3 retrocopies	retro_dnov_1436, retro_dnov_2205, retro_dnov_696,
Gadus morhua	ENSGMOG00000012137	1 retrocopy	retro_gmor_4,
Loxodonta africana	ENSLAFG00000007003	1 retrocopy	retro_lafr_1091,
Pongo abelii	ENSPPYG00000020314	1 retrocopy	retro_pabe_40,
Sus scrofa	ENSSSCG00000021591	1 retrocopy	retro_sscr_842,
Ictidomys tridecemlineatus	ENSSTOG00000027493	1 retrocopy	retro_itri_142,