RetrogeneDB ID: retro_dnov_526

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5730:95221..95900(+)
• Located in intron of: ENSDNOG00000003542

Retrocopy information

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

Parental gene information

• Parental gene symbol: G3BP1
• Ensembl ID: ENSDNOG00000018758
• Aliases: None
• Description: GTPase activating protein (SH3 domain) binding protein 1 [Source:HGNC Symbol;Acc:30292]

Sequence

>retro_dnov_526
TTTTAGGGGAAAAACTCTTCTTATATTCATGTGGGATAGGATTTAAATGGAAAACCAGCAGATGTGGCCTATGGACAGAA
AGAAATCTACAGGAAAGTGATACCACAGAACTTTACCAATGACCATACTAAGATTTGCCATGTTGATGATTTTGCCACTC
TAAATGATGGTGTGGTGGTCCAGGTGATGGGACTGCTTTCTAATAGCAACAAGGTTTTGAGGAGATTCATGCAGACTTTT
GTCCTTGTTCCTGAGGGCTATGTTGCAAATAAGTTCTATTTTACAATGATATCCTCAGATGCCAAGATAAGGTCTTTTGC
TGGCTTTGTCACTGAGCCTCAGGAGGAGTCTGAGGAAGAAGTAGAGGAACTTGAAGAAAGAAAACAGACAACAGAGGTAG
TATCTGATGACTCTGGAACTTTCTATGATCAGACTGTTAGCAAGGACTTGAAAGAACATTTTGAGGAATGGGATACTGAA
CCAGAGCCTAGTCCTAAACTAGAACCAGAGCAAGAACCCATATCTGAGATCCAAGAGGAAAAGTCTGACCCAGTATTAGA
AGAAACTGCTCCTGAGGATGCTCAGAAGACTTCTTCTCCAGCACATAGAAACTTAATTTAGACTGTATAGGAAGAGTTTT
CTTCGGCATCTGTGACAAGTTAAGAACCTTCCTGGTTCT

Alignment

ORF - retro_dnov_526 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.71 %
• Parental protein coverage: 53.01 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FYGKNSSYVHGGLDSNGKPADAVYGQKEIHRKVMSQNFTNCHTKIRHVDAHATLNDGVVVQVMGLLSNNN
          F.GKNSSY.H.G.D.NGKPAD..YGQKEI.RKV..QNFTN.HTKI.HVD..ATLNDGVVVQVMGLLSN.N
Retrocopy F*GKNSSYIHVG*DLNGKPADVAYGQKEIYRKVIPQNFTNDHTKICHVDDFATLNDGVVVQVMGLLSNSN

Parental  QALRRFMQTFVLAPEGSVANKFY-VHNDIFRYQDEV-FGGFVTEPQEESEEEVEEPEERQQTPEVVPEDS
          ..LRRFMQTFVL.PEG.VANKFY...NDI.R.QD.V.F.GFVTEPQEESEEEVEE.EER.QT.EVV..DS
Retrocopy KVLRRFMQTFVLVPEGYVANKFY<FYNDILRCQDKV>FAGFVTEPQEESEEEVEELEERKQTTEVVSDDS

Parental  GTFYDQTVSNDLEEHLEEPVAEPEPDPEPEPEQEPVSEIQEEKSEPVLEEAPPEDPQKNSSPAPADIAQT
          GTFYDQTVS.DL.EH.EE...EPEP.P..EPEQEP.SEIQEEKS.PVLEE..PED.QK.SSPA......T
Retrocopy GTFYDQTVSKDLKEHFEEWDTEPEPSPKLEPEQEPISEIQEEKSDPVLEETAPEDAQKTSSPAHRNLI*T

Parental  VQEDLRTFSWASVTS-KNLPPS
          V.E....FS.ASVTS.KNLP.S
Retrocopy V*EE---FSSASVTS>KNLPGS

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	0.97 RPM	61.26 RPM
SRP012922_cerebellum	0.14 RPM	16.22 RPM
SRP012922_heart	0.00 RPM	18.10 RPM
SRP012922_kidney	0.00 RPM	23.00 RPM
SRP012922_liver	0.00 RPM	16.41 RPM
SRP012922_lung	0.00 RPM	36.35 RPM
SRP012922_quadricep_muscle	0.00 RPM	29.42 RPM
SRP012922_spleen	0.23 RPM	52.88 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_526 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 15 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006626	2 retrocopies	retro_cpor_1119, retro_cpor_464,
Dasypus novemcinctus	ENSDNOG00000018758	3 retrocopies	retro_dnov_1492, retro_dnov_1632, retro_dnov_526 ,
Echinops telfairi	ENSETEG00000017447	1 retrocopy	retro_etel_1488,
Homo sapiens	ENSG00000145907	1 retrocopy	retro_hsap_2322,
Microcebus murinus	ENSMICG00000012235	2 retrocopies	retro_mmur_1247, retro_mmur_1469,
Mustela putorius furo	ENSMPUG00000013661	1 retrocopy	retro_mputfur_625,
Oryctolagus cuniculus	ENSOCUG00000022143	1 retrocopy	retro_ocun_1352,
Otolemur garnettii	ENSOGAG00000001726	2 retrocopies	retro_ogar_3156, retro_ogar_3183,
Pongo abelii	ENSPPYG00000015968	1 retrocopy	retro_pabe_2104,
Pan troglodytes	ENSPTRG00000017438	1 retrocopy	retro_ptro_1696,
Pteropus vampyrus	ENSPVAG00000017250	2 retrocopies	retro_pvam_1188, retro_pvam_188,
Rattus norvegicus	ENSRNOG00000013186	1 retrocopy	retro_rnor_1282,
Tupaia belangeri	ENSTBEG00000004386	12 retrocopies	retro_tbel_2177, retro_tbel_2295, retro_tbel_2296, retro_tbel_2327, retro_tbel_2352, retro_tbel_2460, retro_tbel_2461, retro_tbel_3889, retro_tbel_3928, retro_tbel_4180, retro_tbel_4190, retro_tbel_4246,
Tarsius syrichta	ENSTSYG00000004570	1 retrocopy	retro_tsyr_1391,
Tursiops truncatus	ENSTTRG00000009072	1 retrocopy	retro_ttru_70,