RetrogeneDB ID: retro_dnov_1854

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_33496:83291..84588(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000011241
• Aliases: None
• Description: None

Sequence

>retro_dnov_1854
AAACTCTCTCTCTTGCCTATTACAGTAGACATTCTTGCGGAGACTAGGGTCGGAAAAACAGTGAATAGCTTGCGAAAACG
TGAGCACGTTGGAAACTTTGCCAGGGACTTAGTGGCCCAGTGGAAAAAGTTGGTTCCTGTTGAACAGAGCACTGAGCCTG
AGGAACAGGACTATGAGAAGAGTAATTCCCGAAAGTGCCCCAGGGATGCTCTTCAGAAGGAGGAAGAGATGGAGGGAGAC
TACCAAGAAAACTAGAAAGCTTCTGGTAGCCGATCTTACCACCCTGATCACAGACAGAAAAAGCACAGAAAACTCTCAGA
GCTGGAGAGGGCTCACAAAGACTCTCACAGTCTTGAAAGGAGAGACGAGAGAAAGAGGTGCCAGAGAGTCTCACCAGCTT
ATTCTTCAGACCATGAGTCTTCTGATTATGGCCATGTTCAGTCCCCTCCATCTTCTTCTAGTCCTCATCAGATGTATGTA
GACCATTCCAGATCCCCTGAGGAGGCTCACGAGCCCATCATTTCACACCAGAAACCTGGAAAAGGCCACAGTAATGCCTT
ATAGGACAGACTGGGGGCCAGTCAAGAACACACTTGAGTGAGCCCCAGAGTAAAGGGGTTGTGAGCCAAAACAAAGAGCA
CAGATCTTCCTACAAGAAAAAACGCCCTGTGGATGCCAAGGGAGATGAGAAGTCCTCTGCTATGAGCAGTGAGAAATCAC
ACAAGGTCATCTCCAAAGAGGAGAACCGAAGGCCACCCTCAGAGGAGAGCACAAAGAAGAAACACTCTCTAGTGCTGCCA
AAAAAGAGAAGGAAAGAGAGAGCAGCAGCAGCAAGAAGACGTTTTTACCTCCCCTGGAGTTTGCTTCAGACAACCATCTT
AACAAGCCAAAGCACAAAGACTCAGAGAAAACCGAATGAGACAAAAACAAGTGAAGTCTAGACAGCTTAGAGCTAGGAAG
GGAGACAGGAGACCTGTTACCCAAGGTGGAAGAGAAGGTTTCTAGCACTCTAAAGACTCAAGAAGGGAAACAAAAAACTT
CTAATTTGGATAGAAAGTCAGTGGGCCCCCTCCCTAAAGTTGAGGATGCAGATATGGATGACGAATTTGAGCAGCCCACC
ATGTCTTTCGAGTCATATCTCAGCTATGACCAGCCCCGGAAGAAAAAGAAAAAGATTGTGAAAACATCAGTGACTCCACT
TGGAGAAAAAGGACCTAAAAAAACTGATTCTAAAAGCACTAGTAAAACCTTGGACTTGGTTCAGAAGTTACCTAAGGTGA
ATGAAAGCAAATCAGAG

Alignment

ORF - retro_dnov_1854 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.52 %
• Parental protein coverage: 58.72 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KLSALPITVDILAETGVGKTVNGLRKHEHVGNFARDLVAQWKKLVPVERSTEPDELDYEKSNSRKRPRDA
          KLS.LPITVDILAET.VGKTVN.LRK.EHVGNFARDLVAQWKKLVPVE.STEP.E.DYEKSNSRK.PRDA
Retrocopy KLSLLPITVDILAETRVGKTVNSLRKREHVGNFARDLVAQWKKLVPVEQSTEPEEQDYEKSNSRKCPRDA

Parental  LQKEEEVEGDYQENWKASGSRSYSPDHRQKKHRKLSELERPHKDSHSLERRDERKRCHRVSPAYSSDHES
          LQKEEE.EGDYQEN.KASGSRSY.PDHRQKKHRKLSELER.HKDSHSLERRDERKRC.RVSPAYSSDHES
Retrocopy LQKEEEMEGDYQEN*KASGSRSYHPDHRQKKHRKLSELERAHKDSHSLERRDERKRCQRVSPAYSSDHES

Parental  SDYGHVQSPPSSSSPHQMYVDHSRSPEEDHEPFLSHQKPGKGHSNALQDRLGASRER-HLSEPQSKGVVS
          SDYGHVQSPPSSSSPHQMYVDHSRSPEE.HEP..SHQKPGKGHSNAL.DRLGAS.E..HLSEPQSKGVVS
Retrocopy SDYGHVQSPPSSSSPHQMYVDHSRSPEEAHEPIISHQKPGKGHSNAL*DRLGASQEH<HLSEPQSKGVVS

Parental  -NKEHRSSHKEKRPVDAKGDEKSSALSREKSHKAISKEENRRPLSGESTKEKPP-SSAAKKEKERESSSS
          .NKEHRSS.K.KRPVDAKGDEKSSA.S.EKSHK.ISKEENRRP.S.ESTK.K...SSAAKKEKERESSSS
Retrocopy QNKEHRSSYKKKRPVDAKGDEKSSAMSSEKSHKVISKEENRRPPSEESTKKKHS<SSAAKKEKERESSSS

Parental  KKKFLPPLEFASDNHLKKPKHKDSEKTKSDKNKRSLDGLDLGKGAEDLLPKMKEKVSNALKTQEGKQKTS
          KK.FLPPLEFASDNHL.KPKHKDSEKT..DKNK.SLD.L.LG....DLLPK..EKVS..LKTQEGKQKTS
Retrocopy KKTFLPPLEFASDNHLNKPKHKDSEKTE*DKNK*SLDSLELGRETGDLLPKVEEKVSSTLKTQEGKQKTS

Parental  NLDRKSVGFPPKVEKADMDVELEQPTMSFESYLSYDQ-LKIKKKTVKISMFSLGEKGLMKTDSKSTSKNL
          NLDRKSVG..PKVE.ADMD.E.EQPTMSFESYLSYDQ..K.KKK.VK.S...LGEKG..KTDSKSTSK.L
Retrocopy NLDRKSVGPLPKVEDADMDDEFEQPTMSFESYLSYDQPRKKKKKIVKTSVTPLGEKGPKKTDSKSTSKTL

Parental  DLVQKLPKVNESKSE
          DLVQKLPKVNESKSE
Retrocopy DLVQKLPKVNESKSE

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	4.47 RPM	36.17 RPM
SRP012922_cerebellum	4.12 RPM	22.00 RPM
SRP012922_heart	1.39 RPM	7.66 RPM
SRP012922_kidney	3.01 RPM	18.34 RPM
SRP012922_liver	2.94 RPM	17.96 RPM
SRP012922_lung	5.65 RPM	19.85 RPM
SRP012922_quadricep_muscle	2.08 RPM	16.10 RPM
SRP012922_spleen	7.33 RPM	28.62 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_1854 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011241	1 retrocopy	retro_dnov_1854 ,
Loxodonta africana	ENSLAFG00000017306	1 retrocopy	retro_lafr_424,
Myotis lucifugus	ENSMLUG00000005258	1 retrocopy	retro_mluc_498,
Monodelphis domestica	ENSMODG00000012842	1 retrocopy	retro_mdom_1961,
Sarcophilus harrisii	ENSSHAG00000006165	1 retrocopy	retro_shar_665,