RetrogeneDB ID: retro_dnov_1927

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_3746:50785..51871(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYNCRIP
• Ensembl ID: ENSDNOG00000018345
• Aliases: None
• Description: synaptotagmin binding, cytoplasmic RNA interacting protein [Source:HGNC Symbol;Acc:16918]

Sequence

>retro_dnov_1927
GGTTTGGTGGACGTTATTCTCTATCATCAACCCGATGACAAAAAGAAGAATCGGGGGTTCTGCTTCCTTGAATATGAGGA
TCACAAGTCAGCAGCACAAGCCAGACGCCGGCTGATGAGTGGAAAAGTAAAAGTCTGGGGAAATGTAGTTACAGTTGAAT
GGGCTGACCCTGTGGAAGAACCAGATCCAGAAGTCATGGCTAAGGTGAAAGTTTTATTTGTGAGAAATTTGGCTACTACA
GTGACAGAAGAAATATTGGAGAAGTCATTTTCCGAATTTGGAAAACTTGAAAGAGTGAAGAAGTTGAAAGATTATGCATT
TGTTCATTTTGAGACAGAGGAGCAGCTGTTAAGCGCCATGGATGAAATGAATGGGAAAGAAATAGAAGGGGAAGAAATTG
AAATAGTCTTAGCCAAGCCACCGGACAAGAAAAGGAAAGAGCGCCAAGCTGCTAGACAGGCCTCCAGAAGCACTGCGTAT
GAAGATTATTACTATCACCCTCCTCCTCGCATGCCACCTCCAATTAGAGGTCGGGGTCGTGGTGGGGGGAGAGGTGGATA
TGGCTACCCTCCAGATTACTATGGCTACGAAGATTACTATGATGATTACTATGGTTATGATTATCACGACTATCGTGGAG
GCTATGAAGATCCCTACTACGGCTATGATGATGGCTATGCAGTAAGAGGAAGAGGAGGAGGAAGGGGAGGGCGAGGTGCT
CCACCTCCACCAAGGGGGCGGGGAACACCACCTCCAAGAGGTAGAGCTGGCTATTCTCAAAGGGGGGCACCTTTGGGACC
ACCAAGACGCTCTAGGGGTGGCAGAGGGGGTCCTGCACAACAGCAGAGAGGCCGTGGTTCCCGTGGAGCTCGGGGCAATT
TTGGGGGCAATGTAGGAGGCAAGAGAAAGGCTGATGGGTACAACCAGCCTGATTCCAAGCATCGTCAGACCAACAACCAA
CAGAACTGGGGTTCCCAGCCCATCGCTCAGCAACCGCTTCAGCAAGGTGGTGACTATTCTGGTAACTATGGTTACAATAA
CGACAACCAGGAATTTTATCAGGATACTTATGGGCAACAGTGGAAA

Alignment

ORF - retro_dnov_1927 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.51 %
• Parental protein coverage: 56.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLTDVILYHQPDDKKKNRGFCFL-YEDHKTAAQARRRLMSGKVKVWGNVGTVEWADPIEDPDPEVMAKVK
          GL.DVILYHQPDDKKKNRGFCFL.YEDHK.AAQARRRLMSGKVKVWGNV.TVEWADP.E.PDPEVMAKVK
Retrocopy GLVDVILYHQPDDKKKNRGFCFLEYEDHKSAAQARRRLMSGKVKVWGNVVTVEWADPVEEPDPEVMAKVK

Parental  VLFVRNLANTVTEEILEKAFSHFGKLERVKKLKDYAFIHFDERDGAVKAM-EMNGKDLEG-NIEIV-SKL
          VLFVRNLA.TVTEEILEK.FS.FGKLERVKKLKDYAF.HF........AM.EMNGK..EG..IEIV..K.
Retrocopy VLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFETEEQLLSAMDEMNGKEIEGEEIEIVLAKP

Parental  PDQIR--RKAQRQAAKNQMYDDYYYYGPPHMPPPTRGRGR-GGRGGYGYAPDYYGYEDYY-DYYGYDYHN
          PD..R..R.A.RQA.....Y.DYYY..PP.MPPP.RGRGR.GGRGGYGY.PDYYGYEDYY.DYYGYDYH.
Retrocopy PDKKRKERQAARQASRSTAYEDYYYHPPPRMPPPIRGRGRGGGRGGYGYPPDYYGYEDYYDDYYGYDYHD

Parental  YRGGYEDPYYGYED-FQVGARGRGGRGARGA-APSRGRGAAPPRGRAGYSQRGGP-GSARGVRGARGG-A
          YRGGYEDPYYGY.D...V..RG.GGRG.RGA..P.RGRG..PPRGRAGYSQRG.P.G..R..RG.RGG.A
Retrocopy YRGGYEDPYYGYDDGYAVRGRG-GGRGGRGAPPPPRGRGTPPPRGRAGYSQRGAPLGPPRRSRGGRGGPA

Parental  QQQRGRGVRGARGGRGGNVGGKRKADGYNQPDSKRRQTNN-QNWGSQPIAQQPL-QGGDHSGNYGYKSEN
          QQQRGRG.RGARG..GGNVGGKRKADGYNQPDSK.RQTNN.QNWGSQPIAQQPL.QGGD.SGNYGY...N
Retrocopy QQQRGRGSRGARGNFGGNVGGKRKADGYNQPDSKHRQTNNQQNWGSQPIAQQPLQQGGDYSGNYGYNNDN

Parental  QEFYQDTFGQQWK
          QEFYQDT.GQQWK
Retrocopy QEFYQDTYGQQWK

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	30.34 RPM	67.09 RPM
SRP012922_cerebellum	30.93 RPM	22.68 RPM
SRP012922_heart	13.23 RPM	14.62 RPM
SRP012922_kidney	16.98 RPM	23.00 RPM
SRP012922_liver	10.53 RPM	21.21 RPM
SRP012922_lung	34.52 RPM	36.96 RPM
SRP012922_quadricep_muscle	15.92 RPM	20.08 RPM
SRP012922_spleen	32.96 RPM	45.10 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_1927 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000018345	1 retrocopy	retro_dnov_1927 ,
Homo sapiens	ENSG00000135316	1 retrocopy	retro_hsap_2410,
Macaca mulatta	ENSMMUG00000012575	1 retrocopy	retro_mmul_1843,
Nomascus leucogenys	ENSNLEG00000012879	1 retrocopy	retro_nleu_162,
Oryctolagus cuniculus	ENSOCUG00000000601	1 retrocopy	retro_ocun_1683,
Pongo abelii	ENSPPYG00000016819	1 retrocopy	retro_pabe_1775,
Pan troglodytes	ENSPTRG00000018393	1 retrocopy	retro_ptro_1387,
Rattus norvegicus	ENSRNOG00000000204	1 retrocopy	retro_rnor_805,
Sus scrofa	ENSSSCG00000004294	1 retrocopy	retro_sscr_436,
Vicugna pacos	ENSVPAG00000001061	1 retrocopy	retro_vpac_391,