RetrogeneDB ID: retro_dnov_1348

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_184882:633..1163(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAD2L1
• Ensembl ID: ENSDNOG00000013456
• Aliases: None
• Description: MAD2 mitotic arrest deficient-like 1 (yeast) [Source:HGNC Symbol;Acc:6763]

Sequence

>retro_dnov_1348
ATAGATAGCATTTTATATCAGCCAGGCATACATCCGTCTGAAACCTTTACTTGAATGCAGAAATATGGACTCACCTTGCT
TCAAACTACTGATCCTGAGTTCATAAAATAGCACAGTAATGTGGTGGGACAACTAAAAATTTGGTTATACAAGTGGTCAA
TTCAGAAAGTCGTGGTAGTGATCTCAAATATTGAAAGTGGTAAAGTTCTTGAAAGATGGCAATTTAATATTGAGTGACGA
GACTGCAAAAGAGGACAGTGCACCAGAAAAAAGTCTCAGAAAGCTATCCAAGAGGAAATTCATCCAGTGATCAACAGATC
ACAGCTACAGTAACATTTCTGCCACTAGCAGAAGTTTCTTGTTCATTTGATCACCTAATTTATACAGACAAAGATTTGGT
TGTTCCTGAAAAATGGGAACAGTCAGGACCACAGTTCATTACCAATTCTGTGGAAATGGGTCTTTGTGCATTTACTACCA
CAATTCACAAAATAAGTAGCATGGTGGCCTATAAAATTCCTGTCACTGAC

Alignment

ORF - retro_dnov_1348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.86 %
• Parental protein coverage: 88.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  INSISYQRGIYPSETFTRVQKYGLTLLVTTDPELIKYLNNVVEQLKDWLYKCSVQKLVVVISNIESGEVL
          I.SI.YQ.GI.PSETFT..QKYGLTLL.TTDPE.IK...NVV.QLK.WLYK.S.QK.VVVISNIESG.VL
Retrocopy IDSILYQPGIHPSETFT*MQKYGLTLLQTTDPEFIK*HSNVVGQLKIWLYKWSIQKVVVVISNIESGKVL

Parental  ERWQFDIECDKTAKDDSAPREKSQKAIQDEIRSVI-RQITATVTFLPLLEVSCSFDLLIYTDKDLVVPEK
          ERWQF.IE.....K.....R.KSQKAIQ.EI..VI..QITATVTFLPL.EVSCSFD.LIYTDKDLVVPEK
Retrocopy ERWQFNIE-*RDCKRGQCTRKKSQKAIQEEIHPVI<QQITATVTFLPLAEVSCSFDHLIYTDKDLVVPEK

Parental  WEESGPQFITNSEEVRLRSFTTTIHKVNSMVAYKIPVND
          WE.SGPQFITNS.E..L..FTTTIHK..SMVAYKIPV.D
Retrocopy WEQSGPQFITNSVEMGLCAFTTTIHKISSMVAYKIPVTD

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	3.69 RPM
SRP012922_cerebellum	0.41 RPM	0.55 RPM
SRP012922_heart	0.00 RPM	0.46 RPM
SRP012922_kidney	0.00 RPM	0.55 RPM
SRP012922_liver	0.00 RPM	0.00 RPM
SRP012922_lung	0.15 RPM	1.07 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.17 RPM
SRP012922_spleen	0.00 RPM	5.04 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_1348 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 19 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012813	2 retrocopies	retro_chof_1340, retro_chof_2524,
Dasypus novemcinctus	ENSDNOG00000013456	1 retrocopy	retro_dnov_1348 ,
Erinaceus europaeus	ENSEEUG00000009629	1 retrocopy	retro_eeur_446,
Echinops telfairi	ENSETEG00000015756	1 retrocopy	retro_etel_724,
Homo sapiens	ENSG00000164109	2 retrocopies	retro_hsap_1350, retro_hsap_1707,
Gorilla gorilla	ENSGGOG00000002516	1 retrocopy	retro_ggor_1281,
Loxodonta africana	ENSLAFG00000029619	1 retrocopy	retro_lafr_1138,
Myotis lucifugus	ENSMLUG00000011092	8 retrocopies	retro_mluc_1242, retro_mluc_165, retro_mluc_1802, retro_mluc_1904, retro_mluc_1986, retro_mluc_2434, retro_mluc_609, retro_mluc_696,
Macaca mulatta	ENSMMUG00000004875	2 retrocopies	retro_mmul_1292, retro_mmul_1701,
Monodelphis domestica	ENSMODG00000018944	1 retrocopy	retro_mdom_633,
Mus musculus	ENSMUSG00000029910	2 retrocopies	retro_mmus_1684, retro_mmus_2573,
Nomascus leucogenys	ENSNLEG00000009092	1 retrocopy	retro_nleu_1832,
Oryctolagus cuniculus	ENSOCUG00000008243	4 retrocopies	retro_ocun_1424, retro_ocun_1469, retro_ocun_1486, retro_ocun_752,
Otolemur garnettii	ENSOGAG00000004054	1 retrocopy	retro_ogar_199,
Pongo abelii	ENSPPYG00000015029	2 retrocopies	retro_pabe_1121, retro_pabe_1403,
Pan troglodytes	ENSPTRG00000016401	2 retrocopies	retro_ptro_1156, retro_ptro_925,
Ictidomys tridecemlineatus	ENSSTOG00000025410	2 retrocopies	retro_itri_1592, retro_itri_327,
Tupaia belangeri	ENSTBEG00000011065	3 retrocopies	retro_tbel_4460, retro_tbel_4666, retro_tbel_664,
Tursiops truncatus	ENSTTRG00000011017	1 retrocopy	retro_ttru_1754,