RetrogeneDB ID: retro_dnov_2515

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_81856:3698..4457(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1orf43
• Ensembl ID: ENSDNOG00000019160
• Aliases: None
• Description: chromosome 1 open reading frame 43 [Source:HGNC Symbol;Acc:29876]

Sequence

>retro_dnov_2515
ATGGCGTCCGGCAGTAACTGGCTGTCTGGGGTGAATGTCGTGTTGGTGATGGCCTACGAGAGCCTGGTGTTTGTACTACT
ATTCATTTTTGTGAAGAGGCAAATTATGCGGTTTGCAATGAAATTTCGAAGGGGACCTCATGTCCCTGTGGGACACAATG
CCCCCAAGGACTTGAAAGAAGAGATTGATACGCGACTCTCCAGGGTTCAGGATATCAAGTATGAACCCTAGCTCCTTGCC
GATGATGATACCAGACTGCTTCAGTTGGAAACCCAGGGAAATCAAAATTGCTATAACTATCTGTACAGGATGAAAGCTCT
GGACGCCATCCGTGCCTCTGAGATCCCATTTCATGCTGAAGGCAGGCATGCTCGTTCATTAATGGGCAAGAATTTCCGCT
CCTACTTGCTAGATCTTCGGAACAGTAGTACTCCTTTCAAGGGTGTGCGCAAGGACCTATTTGATACCCTCCTGGATGGC
TATGAGACAGCCCGCTATGGGACAGGGGTCTTTGGCCAGAGTGAGTACCTACGCTATCAGGAGGCCCTGACTGAGCTGGC
CACTGCAGTCAAAGCACAAAGTGGGAGCTCTCAGCGACATCACCAGTCAGCAGCCAAACACCTTACTCAGTCTCTTGAAG
TTTCCCCAACAACCATCCAGGTGACATACCTCCCCTCCAGTCAGAAGAGTAAATGTGCCAAGCACTTCCTGGAGTTGAAG
AGCTTTAAGGACAACTATAACACATTGGAGAGTACTCTG

Alignment

ORF - retro_dnov_2515 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.05 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASGSNWLSGVNVVLVMAYGSLVFVLLFIFVKRQIMRFAMKSRRGPHVPVGHNAPKDLKEEIDMRLSRVQ
          MASGSNWLSGVNVVLVMAY.SLVFVLLFIFVKRQIMRFAMK.RRGPHVPVGHNAPKDLKEEID.RLSRVQ
Retrocopy MASGSNWLSGVNVVLVMAYESLVFVLLFIFVKRQIMRFAMKFRRGPHVPVGHNAPKDLKEEIDTRLSRVQ

Parental  DIKYEPQLLADDDTRLLQLETQGNQNCYNYLYRMKALDAIHASEIPFHAEGRHARSLMGKNFRSYLLDLR
          DIKYEP.LLADDDTRLLQLETQGNQNCYNYLYRMKALDAI.ASEIPFHAEGRHARSLMGKNFRSYLLDLR
Retrocopy DIKYEP*LLADDDTRLLQLETQGNQNCYNYLYRMKALDAIRASEIPFHAEGRHARSLMGKNFRSYLLDLR

Parental  NSSTPFKGVRKALIDTLLDGYETARYGTGVFGQSEYLRYQEALTELATAVKARSGSSQRHHQSAAKDLTQ
          NSSTPFKGVRK.L.DTLLDGYETARYGTGVFGQSEYLRYQEALTELATAVKA.SGSSQRHHQSAAK.LTQ
Retrocopy NSSTPFKGVRKDLFDTLLDGYETARYGTGVFGQSEYLRYQEALTELATAVKAQSGSSQRHHQSAAKHLTQ

Parental  SLEVSPTTIQVTYLPSSQKSKRAKHFLELKSFKDNYNTLESTL
          SLEVSPTTIQVTYLPSSQKSK.AKHFLELKSFKDNYNTLESTL
Retrocopy SLEVSPTTIQVTYLPSSQKSKCAKHFLELKSFKDNYNTLESTL

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	31.89 RPM
SRP012922_cerebellum	0.27 RPM	27.22 RPM
SRP012922_heart	0.70 RPM	21.81 RPM
SRP012922_kidney	0.55 RPM	34.77 RPM
SRP012922_liver	0.46 RPM	19.20 RPM
SRP012922_lung	0.15 RPM	33.29 RPM
SRP012922_quadricep_muscle	0.17 RPM	17.48 RPM
SRP012922_spleen	0.69 RPM	29.19 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_2515 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 13 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011865	1 retrocopy	retro_amel_190,
Callithrix jacchus	ENSCJAG00000009722	1 retrocopy	retro_cjac_175,
Dasypus novemcinctus	ENSDNOG00000019160	1 retrocopy	retro_dnov_2515 ,
Equus caballus	ENSECAG00000017585	2 retrocopies	retro_ecab_618, retro_ecab_814,
Echinops telfairi	ENSETEG00000001056	15 retrocopies	retro_etel_1138, retro_etel_1318, retro_etel_1388, retro_etel_1633, retro_etel_2182, retro_etel_2205, retro_etel_2206, retro_etel_394, retro_etel_651, retro_etel_719, retro_etel_720, retro_etel_773, retro_etel_842, retro_etel_957, retro_etel_981,
Macropus eugenii	ENSMEUG00000002600	6 retrocopies	retro_meug_1149, retro_meug_1298, retro_meug_1439, retro_meug_1637, retro_meug_213, retro_meug_69,
Myotis lucifugus	ENSMLUG00000013338	1 retrocopy	retro_mluc_537,
Monodelphis domestica	ENSMODG00000017237	3 retrocopies	retro_mdom_1283, retro_mdom_2003, retro_mdom_323,
Otolemur garnettii	ENSOGAG00000012008	2 retrocopies	retro_ogar_2563, retro_ogar_38,
Pteropus vampyrus	ENSPVAG00000002717	1 retrocopy	retro_pvam_696,
Rattus norvegicus	ENSRNOG00000017758	1 retrocopy	retro_rnor_139,
Sarcophilus harrisii	ENSSHAG00000012915	1 retrocopy	retro_shar_740,
Tursiops truncatus	ENSTTRG00000015824	1 retrocopy	retro_ttru_923,