RetrogeneDB ID: retro_dnov_2195

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_54798:42557..42974(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CFL2
• Ensembl ID: ENSDNOG00000017048
• Aliases: None
• Description: cofilin 2 (muscle) [Source:HGNC Symbol;Acc:1875]

Sequence

>retro_dnov_2195
GATGATGTGAAAGTAAGAAAATCGACACAAGAGGAGATTACAGAAAGAAAGAAAGCAGTTCTCCCCTATTTAAGCAGTGA
CAACAGACAAATAAGTGTAGAGGAAGCAAAGCAGATCTTAGTGGGTGAAACTGGTGATACTATAGAGGACCCCACACATC
ATCTGTGAAGTTGCTACCTCTGAATGATTGCTGGTATGCTTTGTAAGATGCCATATACGAAATGAAAGATTCTAAGAAAG
AAGTCCTTGTGTTTATATTCTGGGCTCCTGAAAGTTGCACCTTTCAAAAGCAAGATGATTTATGTTGGCTCTAAAGATGC
TATTAAAAAGAAATTTAAGGGTATTTAATATGAGTGGCAAGTAAAAGGCTTTGATGATACTGAGAACCAGTCCACACTTG
GAGAGAAGGGAGGCAAT

Alignment

ORF - retro_dnov_2195 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.43 %
• Parental protein coverage: 90.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NDMKVRKSSTQEEIKKRKKAVLFCLSDDKRQIIVEEAKQILVGDIGDTVEDP-YTSFVKLLPLNDCRYAL
          .D.KVRKS.TQEEI..RKKAVL..LS.D.RQI.VEEAKQILVG..GDT.EDP..TS.VKLLPLNDC.YAL
Retrocopy DDVKVRKS-TQEEITERKKAVLPYLSSDNRQISVEEAKQILVGETGDTIEDP<HTSSVKLLPLNDCWYAL

Parental  YDATYETKESKKEDLVFIFWAPES-APLKSKMIYASSKDAIKKKFTGK-HEWQVNGLNDIKDRSTLGEKL
          .DA.YE.K.SKKE.LVFIFWAPES.AP.KSKMIY..SKDAIKKKF.G...EWQV.G..D....STLGEK.
Retrocopy *DAIYEMKDSKKEVLVFIFWAPES>APFKSKMIYVGSKDAIKKKFKGI*YEWQVKGFDDTENQSTLGEK-

Parental  GGN
          GGN
Retrocopy GGN

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	2.14 RPM
SRP012922_cerebellum	0.00 RPM	5.36 RPM
SRP012922_heart	0.00 RPM	12.99 RPM
SRP012922_kidney	0.00 RPM	0.27 RPM
SRP012922_liver	0.00 RPM	0.00 RPM
SRP012922_lung	0.00 RPM	0.31 RPM
SRP012922_quadricep_muscle	0.00 RPM	63.52 RPM
SRP012922_spleen	0.00 RPM	2.17 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_2195 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 10 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000934	1 retrocopy	retro_dnov_24,
Dasypus novemcinctus	ENSDNOG00000017048	7 retrocopies	retro_dnov_1072, retro_dnov_1379, retro_dnov_1697, retro_dnov_2195 , retro_dnov_2691, retro_dnov_715, retro_dnov_905,
Erinaceus europaeus	ENSEEUG00000013155	4 retrocopies	retro_eeur_335, retro_eeur_448, retro_eeur_513, retro_eeur_578,
Echinops telfairi	ENSETEG00000006010	3 retrocopies	retro_etel_1579, retro_etel_1622, retro_etel_684,
Latimeria chalumnae	ENSLACG00000018011	1 retrocopy	retro_lcha_23,
Macropus eugenii	ENSMEUG00000000739	11 retrocopies	retro_meug_1026, retro_meug_1138, retro_meug_125, retro_meug_1266, retro_meug_1666, retro_meug_1791, retro_meug_2025, retro_meug_2062, retro_meug_210, retro_meug_321, retro_meug_668,
Monodelphis domestica	ENSMODG00000012949	1 retrocopy	retro_mdom_171,
Oryctolagus cuniculus	ENSOCUG00000009383	1 retrocopy	retro_ocun_1397,
Sarcophilus harrisii	ENSSHAG00000004732	1 retrocopy	retro_shar_528,
Tupaia belangeri	ENSTBEG00000000391	2 retrocopies	retro_tbel_29, retro_tbel_4131,