RetrogeneDB ID: retro_dnov_1804

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_31206:21332..21866(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAR1B
• Ensembl ID: ENSDNOG00000013784
• Aliases: None
• Description: SAR1 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:10535]

Sequence

>retro_dnov_1804
CTCTACAAGAAATCTGGAAAACTTGTATTCTTGGGTTTGGACAATGCGGGCAAAACCACTCTTCTACCCATGCTCAAAGA
TGACAGATTGGGCCAACATATTCCAATGCTACATCCAACTTCAGAAGAGTTGACAATTGCTGGAATGACTTTTACAACTT
TTGATCTTGGTGGGCATGAGCAAGCACATTGGGTTTGGAAAAATTACCTCCCAGCAATTAATGGGATTGTCTTTCTGGTG
GACTGTGCAGATCATTCTTGCCTCATGGAATCCAAAGTTGAGCTTAACGCTTTAATGACTGATGAAACAATATACAATGT
GCCAATCTTATTCTTGGGTAACAAAATTAACAGAACAGATGCAATTAGTGAAGAAAAACTCCGTGAGATATTTGGGCTTT
ATGGACAGACCACAGGAAAGGGGAATGTGACCCTGAAGGAACTGAATGCCAGCCCCATGGAAGTCTTCATGTGCAGGTTG
CTCAAGAGGCAAGGCTACGGCGAGGGTTTCCGCTGGCTTTCCCGGTATATTGAC

Alignment

ORF - retro_dnov_1804 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.15 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHVPRR-VWKNYL
          LYKK.GKLVFLGLDNAGKTTLL.MLKDDRLGQH.P.LHPTSEELTIAGMTFTTFDLGGH.....VWKNYL
Retrocopy LYKKSGKLVFLGLDNAGKTTLLPMLKDDRLGQHIPMLHPTSEELTIAGMTFTTFDLGGHEQAHWVWKNYL

Parental  PAINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEAISEERLREMFGLYGQTTGK
          PAINGIVFLVDCADH..L.ESK.EL..LMTDETI.NVPIL.LGNKI.R..AISEE.LRE.FGLYGQTTGK
Retrocopy PAINGIVFLVDCADHSCLMESKVELNALMTDETIYNVPILFLGNKINRTDAISEEKLREIFGLYGQTTGK

Parental  GNVSLKELNARPLEVFMCSVLKRQGYGEGFRWMAQYID
          GNV.LKELNA.P.EVFMC..LKRQGYGEGFRW...YID
Retrocopy GNVTLKELNASPMEVFMCRLLKRQGYGEGFRWLSRYID

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	4.86 RPM	19.06 RPM
SRP012922_cerebellum	2.75 RPM	8.66 RPM
SRP012922_heart	2.09 RPM	15.78 RPM
SRP012922_kidney	0.82 RPM	17.25 RPM
SRP012922_liver	2.94 RPM	28.48 RPM
SRP012922_lung	3.05 RPM	13.59 RPM
SRP012922_quadricep_muscle	4.15 RPM	43.27 RPM
SRP012922_spleen	5.04 RPM	16.14 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_1804 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017849	1 retrocopy	retro_amel_1075,
Dasypus novemcinctus	ENSDNOG00000013784	3 retrocopies	retro_dnov_1584, retro_dnov_1804 , retro_dnov_919,
Equus caballus	ENSECAG00000012409	1 retrocopy	retro_ecab_948,
Loxodonta africana	ENSLAFG00000001021	1 retrocopy	retro_lafr_1043,
Macaca mulatta	ENSMMUG00000004417	3 retrocopies	retro_mmul_1825, retro_mmul_2507, retro_mmul_304,
Oryctolagus cuniculus	ENSOCUG00000008250	1 retrocopy	retro_ocun_1004,
Otolemur garnettii	ENSOGAG00000013347	1 retrocopy	retro_ogar_2472,
Pteropus vampyrus	ENSPVAG00000012433	2 retrocopies	retro_pvam_1219, retro_pvam_725,
Ictidomys tridecemlineatus	ENSSTOG00000011326	1 retrocopy	retro_itri_1714,
Tursiops truncatus	ENSTTRG00000016864	2 retrocopies	retro_ttru_1225, retro_ttru_857,