RetrogeneDB ID: retro_dnov_1745

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_283744:231..678(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRGN
• Ensembl ID: ENSDNOG00000006889
• Aliases: None
• Description: serglycin [Source:HGNC Symbol;Acc:9361]

Sequence

>retro_dnov_1745
CAGTTCCTCAAATGCAGCAGGAGGGTCCTGGCTCTCTCCCTCATCTGCTTTGGGAATCTTCAACTTAAGGTTATCCCACG
TGGAGAGGCAGGTACCAGTGGGTACGCTGCAGTCCAGACAGTAGTTCTGCAAACTGCACTGAGGAAAAGGGACCAATGTT
AGATCTATCTCCTGGAGAATCTGACAGGATCCTTCCCTCCAAGAACTGACCCTTTGCCAATGACGAGATTCCAGAACATG
TACAATGTCTTCCCTCTTTCTGTGGACGATTCTGGATCAGGCTCGGGCTCTGGATTGGGCTCTGGAAACGGCTTTCCAGC
TGAAATCAAACAAGAATACAAACCAAGAGACGATGCTTTCTAATACATTGCTCGGCCTCTCGAGTGGAATCTGCCCTCAA
ACAACCAGCACTTGTATCAGGATGGATCAGAAGATGATTTTATTATA

Alignment

ORF - retro_dnov_1745 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.78 %
• Parental protein coverage: 98.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RFLQSSRLVLALSLLLF-WESSVQGYPMRRGRYQWVRCNPESNSANCIEEGGPMFDLPPGESNRIL-PPR
          .FL..SR.VLALSL..F.WESS..GYP..RGRYQWVRC.P.S.SANC.EE.GPM.DL.PGES.RIL.PPR
Retrocopy QFLKCSRRVLALSLICF<WESST*GYPTWRGRYQWVRCSPDSSSANCTEEKGPMLDLSPGESDRIL>PPR

Parental  TDPFSMTRFQNMRDTFPLSEDYSSGSGSGSGF---NGFPAEIEQEYQAIDEDDAFYYNAQPLERNLPSDN
          TDP..MTRFQNM...FPLS.D..SGSGSGSG....NGFPAEI.QEY.....DDAF.Y.A.PLE.NLPS.N
Retrocopy TDPLPMTRFQNMYNVFPLSVD-DSGSGSGSGLGSGNGFPAEIKQEYK--PRDDAF*YIARPLEWNLPSNN

Parental  QHMDQDGSEDDFII
          QH..QDGSEDDFII
Retrocopy QHLYQDGSEDDFII

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	41.62 RPM
SRP012922_cerebellum	0.00 RPM	3.16 RPM
SRP012922_heart	0.00 RPM	10.67 RPM
SRP012922_kidney	0.00 RPM	6.02 RPM
SRP012922_liver	0.00 RPM	17.18 RPM
SRP012922_lung	0.00 RPM	210.30 RPM
SRP012922_quadricep_muscle	0.00 RPM	4.33 RPM
SRP012922_spleen	0.00 RPM	196.87 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_1745 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 3 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017969	1 retrocopy	retro_amel_82,
Choloepus hoffmanni	ENSCHOG00000000448	9 retrocopies	retro_chof_1085, retro_chof_1907, retro_chof_1936, retro_chof_1950, retro_chof_227, retro_chof_2572, retro_chof_403, retro_chof_876, retro_chof_935,
Dasypus novemcinctus	ENSDNOG00000006889	2 retrocopies	retro_dnov_1745 , retro_dnov_544,