RetrogeneDB ID: retro_dnov_1788

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_3038:131269..131601(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKIRIN2
• Ensembl ID: ENSDNOG00000000549
• Aliases: None
• Description: akirin 2 [Source:HGNC Symbol;Acc:21407]

Sequence

>retro_dnov_1788
GCCACCACTGCCACTAAATGGCAGAAGTATCTCCAAATGGAGCCTTTACCCTTGGGCTACATCTCCCACCTCACCACAGG
ACAAATTCTGTACAGCATTGAGTATAAACACATGCAAAAAAGAAGACATTTAGAAATTAGATTCCAACAGACAGATCCAT
GTCATGCCTCTGCTACACAGCCACATGCATTTCTCCTCAGTGGACCAGCTTCACAGGGACTTCATCTGCAACATCTTCCC
CATTAAAAAAAAAGAAGAGCCCTTGTTTGCTACAGCAAGTTGGGATGATCTGTGAATGTTGAAAAGACCATGAAGAGAAA
GTTTGAGAAGAG

Alignment

ORF - retro_dnov_1788 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.66 %
• Parental protein coverage: 56.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SAAAASPQKYLRMEPSPFGDVSSRLTTEQILYNIKQEYKRMQKRRHLETSFQQTDPCCASDAQPHAFLLS
          ...A...QKYL.MEP.P.G..S..LTT.QILY.I..EYK.MQKRRHLE..FQQTDPC.AS..QPHAFLLS
Retrocopy ATTATKWQKYLQMEPLPLGYIS-HLTTGQILYSI--EYKHMQKRRHLEIRFQQTDPCHASATQPHAFLLS

Parental  GPAS-PGTSSATSSPLKKEQPLFTLRQVGMICERLLKEREEKVREE
          GPAS..GTSSATSSP.........L.QVGMICE...K..EEKV.EE
Retrocopy GPAS<TGTSSATSSPXXXXKSPCLLQQVGMICE-C*KDHEEKV*EE

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	18.86 RPM
SRP012922_cerebellum	0.00 RPM	32.03 RPM
SRP012922_heart	0.00 RPM	11.60 RPM
SRP012922_kidney	0.00 RPM	26.56 RPM
SRP012922_liver	0.15 RPM	19.66 RPM
SRP012922_lung	0.31 RPM	22.15 RPM
SRP012922_quadricep_muscle	0.00 RPM	10.21 RPM
SRP012922_spleen	0.00 RPM	29.76 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_1788 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 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003082	1 retrocopy	retro_cfam_1014,
Choloepus hoffmanni	ENSCHOG00000012160	1 retrocopy	retro_chof_413,
Callithrix jacchus	ENSCJAG00000000769	1 retrocopy	retro_cjac_2231,
Dasypus novemcinctus	ENSDNOG00000000332	3 retrocopies	retro_dnov_1265, retro_dnov_1828, retro_dnov_509,
Dasypus novemcinctus	ENSDNOG00000000549	1 retrocopy	retro_dnov_1788 ,
Homo sapiens	ENSG00000135334	1 retrocopy	retro_hsap_2991,
Gorilla gorilla	ENSGGOG00000002448	1 retrocopy	retro_ggor_2071,
Macaca mulatta	ENSMMUG00000002824	1 retrocopy	retro_mmul_1914,
Pongo abelii	ENSPPYG00000016831	1 retrocopy	retro_pabe_2477,
Pan troglodytes	ENSPTRG00000018409	1 retrocopy	retro_ptro_2023,
Rattus norvegicus	ENSRNOG00000008288	1 retrocopy	retro_rnor_1499,
Sorex araneus	ENSSARG00000006084	1 retrocopy	retro_sara_701,
Sarcophilus harrisii	ENSSHAG00000011555	2 retrocopies	retro_shar_363, retro_shar_579,
Sus scrofa	ENSSSCG00000004307	1 retrocopy	retro_sscr_897,