RetrogeneDB ID: retro_dnov_1905

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_36117:4717..5743(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1GALT1
• Ensembl ID: ENSDNOG00000017353
• Aliases: None
• Description: core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1 [Source:HGNC Symbol;Acc:24337]

Sequence

>retro_dnov_1905
ATGGCCTTTAAATGCTGGCTGAATTTTTTAATCTTGCTCTGTGGATCAGCAATTGGATTTTTTTAATGTTCTCAGCTCGT
TAGTGTTTTCTTGGAAGAACAAAGTGATACGCAACCTAATATTCTTCATAATGATCCTCACACTAGATATTCAGATGACA
ACAGACAGAATCATCTAGAAGGACAGAAGAACGTCAGTGCAGGTGCCAGCCAACATAAAGATGAGGGTGCAGACATTGCT
GAAAAGCTTTATCAGAAGGTTAAAATTCTTTGCTGGGTTATGACAGGCCCTCAAAATCTAGAGAAAAAGGCCAAACATGT
CAAAGCTACATGGGCCAAACATTGCAATAAAGTTTTGTTTATGAGTTCAAAAAATAAAGACTTCCCTACTGTGGGACTAA
AAACCAGAGAAGGCAGAGATCAACTATACTGGAAAACAGTTAAAGCTTTTCGGTATGTTTATGACCATTTTTTGGAAGAT
ACTGATTGGTTTATGAAAGCAGATGATGATACATATGTCATACTAGACAATTTGAGATGGCTTCTTCCAAAATATGATCC
TGAAAAACCCATTTACTTTGGGAGAAGATTTAAGCCCTTTGTAAAGCAGGGCTACATGAGTGGAGGAGCAGGTTACGTAT
TGAGCAAGGAAGCCTTGAAGAGATTTGTGGATGCATTTAAAACATACAAATGTACACACAGTTCCTCCATTGAAGACTTA
GCACTGGGGAGATGCATGGAATTTATAAATGTAGAAGCAGGAGACTCCAGAGATACCACCAGAAAGGAAACTTTTCATCC
TTTTGCACCCAAATACCACTTAATCAAAGGTTATCTGCCCAAAACCTCTTGGTACTGGAAATATAACTATTATCTTGCTG
TAGAGGGTCCGGGATGCTGTTCTGACCTTGCAATTTCTTTTCATTACGTTGACCCTCTAACTATGTATGAGTTAGAATAC
CTCATTTATCATCTTCGCCCATATGGTTATTTATACAGATATCAACCTGCCTTACCAGAGAATATA

Alignment

ORF - retro_dnov_1905 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.01 %
• Parental protein coverage: 94.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASKSWLNVLIFLCGSAVGFFLCSQLFSTLLEEQSDTQPNILHNDPHARHSDDNGQHHLEGQMNFNADVN
          MA.K.WLN.LI.LCGSA.GFF.CSQL.S..LEEQSDTQPNILHNDPH.R.SDDN.Q.HLEGQ.N..A...
Retrocopy MAFKCWLNFLILLCGSAIGFF*CSQLVSVFLEEQSDTQPNILHNDPHTRYSDDNRQNHLEGQKNVSAGAS

Parental  QHKDEDTDIAEKLYQKVKILCWVMTGPQNLEKKAKHVKATWAQRCNKVLFMSSEENKDFPTVGLKTKEGR
          QHKDE..DIAEKLYQKVKILCWVMTGPQNLEKKAKHVKATWA..CNKVLFMSS..NKDFPTVGLKT.EGR
Retrocopy QHKDEGADIAEKLYQKVKILCWVMTGPQNLEKKAKHVKATWAKHCNKVLFMSSK-NKDFPTVGLKTREGR

Parental  DQLYWKTIKAFQYVYDHYLEDADWFMKADDDTYVILDNLRWLLSKYDPQNPIYFGRRFKPFVKQGYMSGG
          DQLYWKT.KAF.YVYDH.LED.DWFMKADDDTYVILDNLRWLL.KYDP..PIYFGRRFKPFVKQGYMSGG
Retrocopy DQLYWKTVKAFRYVYDHFLEDTDWFMKADDDTYVILDNLRWLLPKYDPEKPIYFGRRFKPFVKQGYMSGG

Parental  AGYVLSKEALKRFVDAFKTEKCTHSSSIEDLALGRCMEIMNVEAGDSRDTTGKETFHPFVPEHHLIKGYL
          AGYVLSKEALKRFVDAFKT.KCTHSSSIEDLALGRCME..NVEAGDSRDTT.KETFHPF.P..HLIKGYL
Retrocopy AGYVLSKEALKRFVDAFKTYKCTHSSSIEDLALGRCMEFINVEAGDSRDTTRKETFHPFAPKYHLIKGYL

Parental  PKTFWYWNYNYYPTVEGPGCCSDLAISFHYVDPLTMYELEYLVYHLRPY-YLYRY-PALPENV
          PKT.WYW.YNYY..VEGPGCCSDLAISFHYVDPLTMYELEYL.YHLRPY.YLYRY.PALPEN.
Retrocopy PKTSWYWKYNYYLAVEGPGCCSDLAISFHYVDPLTMYELEYLIYHLRPYGYLYRYQPALPENI

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	12.64 RPM	109.10 RPM
SRP012922_cerebellum	0.00 RPM	1.37 RPM
SRP012922_heart	0.00 RPM	2.09 RPM
SRP012922_kidney	0.00 RPM	18.07 RPM
SRP012922_liver	0.15 RPM	5.73 RPM
SRP012922_lung	0.15 RPM	3.51 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.38 RPM
SRP012922_spleen	0.57 RPM	9.27 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_1905 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000225	2 retrocopies	retro_chof_1782, retro_chof_2581,
Dasypus novemcinctus	ENSDNOG00000017353	2 retrocopies	retro_dnov_1801, retro_dnov_1905 ,
Homo sapiens	ENSG00000106392	2 retrocopies	retro_hsap_3177, retro_hsap_4065,
Loxodonta africana	ENSLAFG00000000063	1 retrocopy	retro_lafr_1166,
Myotis lucifugus	ENSMLUG00000014789	1 retrocopy	retro_mluc_1310,
Macaca mulatta	ENSMMUG00000016338	1 retrocopy	retro_mmul_2009,
Oryctolagus cuniculus	ENSOCUG00000026002	1 retrocopy	retro_ocun_216,
Otolemur garnettii	ENSOGAG00000012847	1 retrocopy	retro_ogar_855,
Petromyzon marinus	ENSPMAG00000001562	1 retrocopy	retro_pmar_2,
Pan troglodytes	ENSPTRG00000018925	2 retrocopies	retro_ptro_2266, retro_ptro_2755,