RetrogeneDB ID: retro_dnov_960

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_1276:114105..115071(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IK
• Ensembl ID: ENSDNOG00000009727
• Aliases: None
• Description: IK cytokine, down-regulator of HLA II [Source:HGNC Symbol;Acc:5958]

Sequence

>retro_dnov_960
TTCTCCAACCCTTTGGCCCCAGATAGCTACGATGTGGATGATCCTCACTCCTTCCACCAATCAAAACTCAGCAATGGAGA
CTTCAGGAAGCTTTTCATGACCCCAAGGGCAGCACCCACCTTGGCATGTCCCTCTAAGTCATGTCACCATAAGATGCCAA
GGGAGTACAATAAGGATGTAGACCCAGCTACAGGAAGGAGGAAAAACAAAAGTTATTATGCCAAGCTACACCAGCAAGAA
ATTGAGAGAGAGCGGGAGCTAGCAAAGAAGTACCGGGACCGTGCCAAGGAACGGAGAGATGGGGTGAACAAATATTATGA
AGAAACTGAGCTGATCTACACCACAGCTAACTACAGAGCTGTGGGTCCCACTGGTGAGGTGAATGAATCAGCTGCAGAGA
AGAGAAGACAGTTGATCCAGAAGTCAAAATTCTTGGGTGGTGATATGGAACACACCCATTTGGTGAAAGGCTTGGATTTT
GCTTTGCTTCAGAAGGTACGAGCTGATGTTGCCAGCAAAGAAAAAGAGGAGGAAGAACTGATGAAAAAGCCCCCAGAAGA
AACCAAGAAAGATGAAGATCCTGAGAATAACATTGAATTTAAAACACACCTGGGTCGCAATGTTTATAACATACTCTTCA
AGAGCAAAGCATATGAGTGGAATGAGCTGTTCCTGCCGGGCCGCATGGCTTATGTGGTGGACTTGGCTGATGAATCTGCT
GACACGGACATTCCCACCACTCTTATTCGCAGCAAGGCTGATTGCCCATCCACCGAGACCCTGACCACACTGACCACAAA
TGACATTGTCATTAATAAGCTCACCCAGATATTTTCCTACCTGAGGCAGAGTACCCATAATAAGAAGCTCAAGAAGAAAG
ATAAAGGGAAGTTGGAAGAGAAGAAACCTCTTGAGGCTGATATGAACATTTTTGAGGACATTGGAGATTATGTGCCCTCC
TTGACC

Alignment

ORF - retro_dnov_960 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.02 %
• Parental protein coverage: 57.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FSNPLAPDGHDVDDPHSFHQSKLTNEDFRKLLMTPRAAPTSAPPSKSRHHEMPREYNEDEDPAARRRKKK
          FSNPLAPD..DVDDPHSFHQSKL.N.DFRKL.MTPRAAPT.A.PSKS.HH.MPREYN.D.DPA..RRK.K
Retrocopy FSNPLAPDSYDVDDPHSFHQSKLSNGDFRKLFMTPRAAPTLACPSKSCHHKMPREYNKDVDPATGRRKNK

Parental  SYYAKLRQQEIERERELAEKYRDRAKERRDGVNKDYEETELISTTANYRAVGPTAEADKSAAEKRRQLIQ
          SYYAKL.QQEIERERELA.KYRDRAKERRDGVNK.YEETELI.TTANYRAVGPT.E...SAAEKRRQLIQ
Retrocopy SYYAKLHQQEIERERELAKKYRDRAKERRDGVNKYYEETELIYTTANYRAVGPTGEVNESAAEKRRQLIQ

Parental  ESKFLGGDMEHTHLVKGLDFALLQKVRAEIASKEKEEEELMEKPQKETKKDEDPENKIEFKTRLGRNVYR
          .SKFLGGDMEHTHLVKGLDFALLQKVRA..ASKEKEEEELM.KP..ETKKDEDPEN.IEFKT.LGRNVY.
Retrocopy KSKFLGGDMEHTHLVKGLDFALLQKVRADVASKEKEEEELMKKPPEETKKDEDPENNIEFKTHLGRNVYN

Parental  MLFKSKAYERNELFLPGRMAYVVDLDDEYADTDIPTTLIRSKADCPTMEAQTTLTTNDIVISKLTQILSY
          .LFKSKAYE.NELFLPGRMAYVVDL.DE.ADTDIPTTLIRSKADCP..E..TTLTTNDIVI.KLTQI.SY
Retrocopy ILFKSKAYEWNELFLPGRMAYVVDLADESADTDIPTTLIRSKADCPSTETLTTLTTNDIVINKLTQIFSY

Parental  LRQGTRNKKLKKKDKGKLEEKKPPEADMNIFEDIGDYVPSTT
          LRQ.T.NKKLKKKDKGKLEEKKP.EADMNIFEDIGDYVPS.T
Retrocopy LRQSTHNKKLKKKDKGKLEEKKPLEADMNIFEDIGDYVPSLT

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	92.76 RPM
SRP012922_cerebellum	0.00 RPM	131.01 RPM
SRP012922_heart	0.00 RPM	46.17 RPM
SRP012922_kidney	0.00 RPM	79.40 RPM
SRP012922_liver	0.00 RPM	61.61 RPM
SRP012922_lung	0.00 RPM	125.23 RPM
SRP012922_quadricep_muscle	0.00 RPM	44.66 RPM
SRP012922_spleen	0.00 RPM	131.52 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_960 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 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009727	3 retrocopies	retro_dnov_618, retro_dnov_714, retro_dnov_960 ,
Dipodomys ordii	ENSDORG00000006584	4 retrocopies	retro_dord_128, retro_dord_130, retro_dord_134, retro_dord_139,
Homo sapiens	ENSG00000113141	1 retrocopy	retro_hsap_2262,
Gorilla gorilla	ENSGGOG00000013374	1 retrocopy	retro_ggor_1685,
Loxodonta africana	ENSLAFG00000008152	1 retrocopy	retro_lafr_362,
Otolemur garnettii	ENSOGAG00000014281	1 retrocopy	retro_ogar_1402,
Pongo abelii	ENSPPYG00000015861	1 retrocopy	retro_pabe_1954,
Sorex araneus	ENSSARG00000007388	3 retrocopies	retro_sara_416, retro_sara_419, retro_sara_558,