RetrogeneDB ID: retro_dnov_2267

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_5994:37042..37474(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POU5F2
• Ensembl ID: ENSDNOG00000003949
• Aliases: None
• Description: POU domain class 5, transcription factor 2 [Source:HGNC Symbol;Acc:26367]

Sequence

>retro_dnov_2267
TTTGCCACGCTCCTGAAGCAGAGGCGCATCACCCTGGGGTACACCCAGGCCAACGTGGGGCTCACCCTGGGGGTGCTTTC
TGGGAAGGTGTTCAGCCAGACGACCATCTGCTGCTGCTTCGGGGCCCTGCAGCGGAGCTTCAAGAACATGCGCAAGCTGC
GGCCTCTGCTCCAGCGGTGGGTGGAGGAGGCCGACAACCAGAACCTCCAGGAGATATGCAAAACGGAGACCCTCCTGCAG
CAGGCCCGGAAGTGAAAGCGGCCGAGCACTGAGAGCAGAATGAGGGGCAACCTGGAGAGCATGTTCCTGCAGTGCCCAAA
GCCCATGCTGCAGACCAGCCACGTCGCCCAGCAGCTCGGGCTGGAGAAGGTCGTGGGCCCAGTGTGGTTCTGTAACCGGC
GCCAGAAGGGCAAGCGCTCGAGCAGTGACTGT

Alignment

ORF - retro_dnov_2267 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.56 %
• Parental protein coverage: 68.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICR-FEALQLSFKNMCKLRPLLQKWVEEADSNENL
          FA.LLKQ.RITLGYTQA.VGLTLGVL.GKVFSQTTIC..F.ALQ.SFKNM.KLRPLLQ.WVEEAD.N.NL
Retrocopy FATLLKQRRITLGYTQANVGLTLGVLSGKVFSQTTICCCFGALQRSFKNMRKLRPLLQRWVEEAD-NQNL

Parental  QEICKTETLLQQARKRKRTSIENRVRGNLESMFLQCPKPTLQQISHIAQQLGLEKDVVRVWFCNRRQKGK
          QEICKTETLLQQARK.KR.S.E.R.RGNLESMFLQCPKP.L.Q.SH.AQQLGLEK.V..VWFCNRRQKGK
Retrocopy QEICKTETLLQQARK*KRPSTESRMRGNLESMFLQCPKPML-QTSHVAQQLGLEKVVGPVWFCNRRQKGK

Parental  RSSSDC
          RSSSDC
Retrocopy RSSSDC

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	0.00 RPM
SRP012922_cerebellum	0.00 RPM	0.00 RPM
SRP012922_heart	0.00 RPM	0.00 RPM
SRP012922_kidney	0.00 RPM	0.00 RPM
SRP012922_liver	0.00 RPM	0.00 RPM
SRP012922_lung	0.00 RPM	0.15 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.00 RPM
SRP012922_spleen	0.00 RPM	0.23 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_2267 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010377	3 retrocopies	retro_amel_1057, retro_amel_1213, retro_amel_1616,
Bos taurus	ENSBTAG00000021111	2 retrocopies	retro_btau_1576, retro_btau_951,
Callithrix jacchus	ENSCJAG00000019789	1 retrocopy	retro_cjac_123,
Dasypus novemcinctus	ENSDNOG00000003949	1 retrocopy	retro_dnov_2267 ,
Dipodomys ordii	ENSDORG00000009549	1 retrocopy	retro_dord_65,
Macropus eugenii	ENSMEUG00000013221	3 retrocopies	retro_meug_1146, retro_meug_1475, retro_meug_692,
Mustela putorius furo	ENSMPUG00000001202	2 retrocopies	retro_mputfur_253, retro_mputfur_96,
Mus musculus	ENSMUSG00000024406	2 retrocopies	retro_mmus_2201, retro_mmus_250,
Oryctolagus cuniculus	ENSOCUG00000017160	3 retrocopies	retro_ocun_1175, retro_ocun_1696, retro_ocun_463,
Ictidomys tridecemlineatus	ENSSTOG00000026103	3 retrocopies	retro_itri_1076, retro_itri_1705, retro_itri_951,