RetrogeneDB ID: retro_dnov_879

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_11757:82558..83126(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSR1
• Ensembl ID: ENSDNOG00000015772
• Aliases: None
• Description: signal sequence receptor, alpha [Source:HGNC Symbol;Acc:11323]

Sequence

>retro_dnov_879
TTTCTAGTAAATAACTTCCTGAAGTTCATGGTAGGCTTTACAAATAAGGGTACAGTAGAATTTATTGTTGAATCCCTAGT
GCCTCATTCCGTTACCCTTAGGACTACCAGTTTTATATCCAGAATTTCACAGCTCTTCCTCTGAACCCTGTAGTGCTACC
CCAGAGACAGGCAACATTTGAGTACTCCTTCATCCCTGCAGAGCCCTGGGTGGGTGAACTTTTGGTCTAGTCATCAATCT
GAAGTACAAAGATCTGAGTAGCAGTGTATTCCAAGATGCTGTCTTCAATCAAACAGTTACAATTACTGAAAGAGAGGATG
GGTTAGATGGAGAAACAGTCTTGTTCCTTATCAGTCTTAGGCTGGCAGTTGTTGCTGTGCTGGCCTTCATCAACTCTTAG
AATCTAAAATGCAAAAGACTGATACATAAAGTAGAAATAGGTACATCAAATCAGAAAAATGTTGATATGAGTTGTATTCC
TTGGAAAACTTTGAATCAGATCAATAAAGTTTCACCAAGAAGATTGCCCTGGAAACAGGCACAGGAAAAACCAGTGGGAT
CTGATGAG

Alignment

ORF - retro_dnov_879 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.28 %
• Parental protein coverage: 67.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FPANNIVKFLVGFTNKGTEDFIVESL-DASFRYPQDYQFYIQNFTALPLNTVVPPQRQATFEYSFIPAEP
          F..NN..KF.VGFTNKGT..FIVESL..ASFRYP.DYQFYIQNFTALPLN.VV.PQRQATFEYSFIPAEP
Retrocopy FLVNNFLKFMVGFTNKGTVEFIVESL<SASFRYP*DYQFYIQNFTALPLNPVVLPQRQATFEYSFIPAEP

Parental  -MGGRPFGLVINLNYKDLNGNVFQDAVFNQTVTIIEREDGLDGETIFMYMFLAGLGLLVVVGLHQLLE-S
          ..GG..FGLVINL.YKDL...VFQDAVFNQTVTI.EREDGLDGET.....FL..L.L.VV..L.......
Retrocopy <LGG*TFGLVINLKYKDLSSSVFQDAVFNQTVTITEREDGLDGETV---LFLISLRLAVVAVLAFINS*N

Parental  RKRKRTIQKVEMGTSSQNDVDMSWIPQETLNQINKASPRRLPRKRAQKRSVGSDE
          .K.KR.I.KVE.GTS.Q..VDMS.IP..TLNQINK.SPRRLP.K.AQ...VGSDE
Retrocopy LKCKRLIHKVEIGTSNQKNVDMSCIPWKTLNQINKVSPRRLPWKQAQEKPVGSDE

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	64.95 RPM
SRP012922_cerebellum	0.00 RPM	15.12 RPM
SRP012922_heart	0.00 RPM	14.85 RPM
SRP012922_kidney	0.00 RPM	30.94 RPM
SRP012922_liver	0.15 RPM	31.12 RPM
SRP012922_lung	0.31 RPM	34.82 RPM
SRP012922_quadricep_muscle	0.17 RPM	17.48 RPM
SRP012922_spleen	0.11 RPM	48.07 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_879 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000022731	1 retrocopy	retro_btau_1285,
Dasypus novemcinctus	ENSDNOG00000015772	1 retrocopy	retro_dnov_879 ,
Equus caballus	ENSECAG00000019520	1 retrocopy	retro_ecab_399,
Echinops telfairi	ENSETEG00000020111	1 retrocopy	retro_etel_1983,
Oryctolagus cuniculus	ENSOCUG00000009083	1 retrocopy	retro_ocun_1388,
Otolemur garnettii	ENSOGAG00000014234	1 retrocopy	retro_ogar_1465,
Ictidomys tridecemlineatus	ENSSTOG00000022608	1 retrocopy	retro_itri_1850,