RetrogeneDB ID: retro_dnov_624

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_6933:4275..4842(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAK16
• Ensembl ID: ENSDNOG00000008424
• Aliases: None
• Description: MAK16 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:13703]

Sequence

>retro_dnov_624
AAAAACATTTGTTCCTTCAAAATGAGAACCAAGACTCAGGGCTTTTTCAGAAATGAATACAGCCTAACTGGATTATGCAG
TCGGTCATCCTGTCCCATGGAAAACTGTCAATACGCCACTATCAAAGAAGAAAAAGGACAGTGCTAGTATATGAAGGTTA
TAGAATGAGTAGCTTTTCCTAGGCATCTCTAGGAACAGGTTTGGCTCAGTAAAAACTATGAGAAAGCACTGGGGCAAATA
GATGAAAATCTAATTTACTGGCTTCATTTCATTAGACATAATAAATATAAGCAGAGATTCACCAAGATCACCCAGTACCT
AATACGAGTTCGAAACCTTATATTAAAGTGACAGAGGAAACTTGTTCCTTTGAGTAAGAAGGTGGAACAGAGGGAGAAAA
GAGAGGAAAAGGCATTTGTAGCTGCTCAGCCTGATAATGCTATTGAAAAGGAATTATTGGAGAGACTGAAACAAGATATC
TAGGGCAACATGTACAACTTCCTTGTTCATGCCTTTGACAAAGCCCTGGAACAGCAGGGGGTGGAGAGTGATTCTTCAGA
TGCTGAG

Alignment

ORF - retro_dnov_624 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.92 %
• Parental protein coverage: 65.07 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KQFCSFKLSSKTQRFYRNEYSLTELCNQSSCPLPNRQCTTMKEEKGQCYLFMKVIERAAFPRRLWERVRL
          K..CSFK...KTQ.F.RNEYSLT.LC..SSCP..N.Q..T.KEEKGQC...MKVIE..AFPR.L.E.V.L
Retrocopy KNICSFKMRTKTQGFFRNEYSLTGLCSRSSCPMENCQYATIKEEKGQC*-YMKVIE*VAFPRHL*EQVWL

Parental  SKNYEKALEQIDENLIYWPQFIRH-KCKQRFTKITQYLIRIRKLTLKRQRKLVPLSKKVERREKRREEKA
          SKNYEKAL.QIDENLIYW..FIRH.K.KQRFTKITQYLIR.R.L.LK.QRKLVPLSKKVE.REKR.EEKA
Retrocopy SKNYEKALGQIDENLIYWLHFIRHNKYKQRFTKITQYLIRVRNLILK*QRKLVPLSKKVEQREKR-EEKA

Parental  LVAAQLDNAIEKELLERLKQDTYGDIYNFPIHAFDKALEQQEAESDSSDAE
          .VAAQ.DNAIEKELLERLKQD..G..YNF..HAFDKALEQQ..ESDSSDAE
Retrocopy FVAAQPDNAIEKELLERLKQDI*GNMYNFLVHAFDKALEQQGVESDSSDAE

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	24.89 RPM
SRP012922_cerebellum	0.00 RPM	22.96 RPM
SRP012922_heart	0.00 RPM	8.59 RPM
SRP012922_kidney	0.00 RPM	15.61 RPM
SRP012922_liver	0.00 RPM	12.85 RPM
SRP012922_lung	0.00 RPM	27.03 RPM
SRP012922_quadricep_muscle	0.00 RPM	9.17 RPM
SRP012922_spleen	0.00 RPM	34.11 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_624 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009081	5 retrocopies	retro_chof_2336, retro_chof_2538, retro_chof_531, retro_chof_867, retro_chof_948,
Dasypus novemcinctus	ENSDNOG00000008424	1 retrocopy	retro_dnov_624 ,
Latimeria chalumnae	ENSLACG00000018758	1 retrocopy	retro_lcha_67,
Macropus eugenii	ENSMEUG00000006945	1 retrocopy	retro_meug_1291,
Myotis lucifugus	ENSMLUG00000002758	1 retrocopy	retro_mluc_590,
Oryctolagus cuniculus	ENSOCUG00000008735	3 retrocopies	retro_ocun_1053, retro_ocun_1298, retro_ocun_908,
Sus scrofa	ENSSSCG00000015832	1 retrocopy	retro_sscr_917,