RetrogeneDB ID: retro_dnov_340

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3797:222727..223689(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABPB2
• Ensembl ID: ENSDNOG00000004312
• Aliases: None
• Description: GA binding protein transcription factor, beta subunit 2 [Source:HGNC Symbol;Acc:28441]

Sequence

>retro_dnov_340
AATGGTGCAGATGTGAATGCCAAAGACATGCTGAAGATGACAGCTTTGCATTGGGCCACAGAGCACCACCATCGAGATGC
TGTAGAGCTACTTATTAAGTATGGAGCTGATGTCCATGCTTTCAGCAAATTTGATAAATCTGCCTTTGACATAGCCCCTG
GAGAAGAACAATGCTGAGATTCTGGTCATCCTCCAGGAAGCAATGCAGAATCAGGTGAATGCTAATCCCGAGAGAACCAA
TCCTGTGACTAACTCTGTGAGTATGGCTGCTCCATTTATCTTCACATCTGGGAGAAGTTGTCAACCTTGCTAGCCTTGTT
TCTTCAGCCAACACCAAAACAACCTCAGGTGACCCCCATGCCTCAACAGTACAGTTCTCAAATTATACCACCTCAGTGCT
GGCCACCCTTGCAGCTCTTGCTGAGGCATCAGCCCCCCTCTCCAACTCACACAGAGCCACAGCCAATTCAGAGGAAATCA
TAGAGGGAAATTCTGTTGATCCCTCAGTCCAGCAAATGATGGGGAGTGGAGGCCAGAGAGTCATTACCATAGTGACTGAT
GGAGTCCCTCTGGGTAATCTTCAAACTGCAATCCCTACTGGAGGCATTGGCCAGCCATTTATTGTAACAATGCAAGATGG
ACAGCAAGTTCTAACTGTACCTGCTGGTCAGGTTGCAGAGGAGACCGTAATTGAAGAGGAGGAAGAAGACGAAGAAAAGT
TGCCACTGACTAAGAAACCAAGGATAGAAGAGATAATAAACAGTGTGGAGGAAAGGAAGGAAGGCAGTGAAAGAGAGCTG
CTACAGCAGCAGCTCCAGGAGGCCAATCGAAGAGCCCAGGAATACCGACACCAGCTTCTAAAGAAAGAGCAGGAGGCAGA
ACAGTACCGCCTCAAATTGGAAGCCATGGCCCGGCAACAACCCAATGGAGTTGATATTACCATGGTTGAAGAGGTGGCTG
AG

Alignment

ORF - retro_dnov_340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.45 %
• Parental protein coverage: 71.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NGADVNAKDMLKMTALHWATEHHHRDVVELLIKYGADVHAFSKFDKSAFDIA-LEKNNAEILVILQEAMQ
          NGADVNAKDMLKMTALHWATEHHHRD.VELLIKYGADVHAFSKFDKSAFDIA.LEKNNAEILVILQEAMQ
Retrocopy NGADVNAKDMLKMTALHWATEHHHRDAVELLIKYGADVHAFSKFDKSAFDIA>LEKNNAEILVILQEAMQ

Parental  NQVNANPERTNPVTNSVSMAAPFIFTSG-EVVNLASLVSSANTKTTSGDPHASTVQFSNYTTSVLATLAA
          NQVNANPERTNPVTNSVSMAAPFIFTSG.EVVNLASLVSSANTKTTSGDPHASTVQFSNYTTSVLATLAA
Retrocopy NQVNANPERTNPVTNSVSMAAPFIFTSG>EVVNLASLVSSANTKTTSGDPHASTVQFSNYTTSVLATLAA

Parental  LAEASAPLSNSHRATANSEEIIEGNSVDPSIHQMMGSGGQRVITIVTDGVPLGNLQTAIPTGGIGQPFIV
          LAEASAPLSNSHRATANSEEIIEGNSVDPS..QMMGSGGQRVITIVTDGVPLGNLQTAIPTGGIGQPFIV
Retrocopy LAEASAPLSNSHRATANSEEIIEGNSVDPSVQQMMGSGGQRVITIVTDGVPLGNLQTAIPTGGIGQPFIV

Parental  TMQDGQQVLTVPAGQVAEETVIEEEEEDEEKLPLTKKPRIEEIINSVEERKEGSERELLQQQLQEANRRA
          TMQDGQQVLTVPAGQVAEETVIEEEEEDEEKLPLTKKPRIEEIINSVEERKEGSERELLQQQLQEANRRA
Retrocopy TMQDGQQVLTVPAGQVAEETVIEEEEEDEEKLPLTKKPRIEEIINSVEERKEGSERELLQQQLQEANRRA

Parental  QEYRHQLLKKEQEAEQYRLKLEAMARQQPNGVDITMVEEVAE
          QEYRHQLLKKEQEAEQYRLKLEAMARQQPNGVDITMVEEVAE
Retrocopy QEYRHQLLKKEQEAEQYRLKLEAMARQQPNGVDITMVEEVAE

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	1.17 RPM	6.22 RPM
SRP012922_cerebellum	0.82 RPM	5.22 RPM
SRP012922_heart	0.00 RPM	3.25 RPM
SRP012922_kidney	0.55 RPM	2.19 RPM
SRP012922_liver	0.77 RPM	2.94 RPM
SRP012922_lung	0.92 RPM	8.86 RPM
SRP012922_quadricep_muscle	0.52 RPM	1.73 RPM
SRP012922_spleen	2.06 RPM	12.13 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_340 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004312	1 retrocopy	retro_dnov_340 ,