RetrogeneDB ID: retro_rnor_1733

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 20:34956713..34957928(+)
• Located in intron of: ENSRNOG00000033891

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tbrg1
• Ensembl ID: ENSRNOG00000023850
• Aliases: None
• Description: Transforming growth factor beta regulator 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5PQK8]

Sequence

>retro_rnor_1733
ATGAGCGTGTTGAGCGGCCTGGCTTCCGAGCCGCGCACCCCGCTGTCCAGCAAGGCCAGGATGAAAAGGCTCCCGAAGAA
GAACCAGAATGAGAAGTACCGGTTGAAGTACCTGCGGCTGCGCAGAGCAGCTAAGGCCACGGTGTTTGAGAATGCTGTTT
GTGATGAAATTGCTCGTCTTGAGGAAAAATTCCTTAAAGCAAAGGAGGAAAGAAGATACTTGCTGAAGAAGCTCCTCCAG
ATCCATGCTCTAACTGAAGGGGAACCACAGGCTGCCGCTCCTTCCCACAGCTCCAGTTTGCCCCTGGCTTATGGTGTCAC
CAGCTCTGTGGGAACCATCCAGGGAGCCGGGCCCAGCACTGGGGCCGAGGAACCATTTGCGAAGAAATCCAAGAAGGAGA
AGAAAGAAAAGGGCAAAGAGAACAGCAAACTGGAAGTGCTGAAGAAAACATCCAAGAGAAAGAAAATGGAGGGAAATGCT
CGCAAGCTGGTCCGGCCCATTGCCCTGGATCCCTCAGGACAGCCTGTGTTCCCCATCGGACTAGGGGGTCTGACAGTATA
TAGCCTGGGGGAGATCATCACCAACCGACCCGGCTTCCATGATGAGAATGCCATCTATCCTGTGGGCTACTGCAGCACTC
GAGTGTACGCCAGCATGAAGTGCCCAGACCAGAAGTGCCTATATACCTGTCAGATCAAGGATGGCGGTGTACAGCCTCAG
TTTGAAATCGTTCCTGAAGATGACCCCCGGAATACCATCGTTGGCTCCTCTGCAGATGCCTGTTACGAAGAACTGCTCAG
GGCCATCAGTGCCGCAACGGGGAAACTGATGCCTAACCCACTTTCATGTGGCGCCGACTTCTTTGGGTTTTCTCATCCAA
CCATCCATAACCTGATTCAGAGTTGTCCAGAAGCTCAGAACTGCGTCAATTACCAGTGGGTGAAATTCGATGCGTGCAAA
CCCAGGAAGGGGCAGCTCTCTCAGGAGCTGCCAGAGAATGATGCAGCTATGAGCCTTGAAGCCTTTCCGACACAGACGTT
TGATGATGACCATGAGGATTCCATTCTGCCAGGCTCCCTGGACCTGCCTGAGCTTCAGCATGAAGCCTTCGTGTCGTCTT
ACCAGCCCGAGTTCCTGACACATGAACCCTTGGTTGACACTGACCTGCAGCACCTCAAGTCTCCATCCCAGTGTAGCCCA
ATTCAGTCTTCAGAC

Alignment

ORF - retro_rnor_1733 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.51 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVLSGLASEPRTPLSSKARMKRLPKKNQNEKYRLKYLRLRRAAKATVFENAAVCDEIARLEEKFLKAKE
          MSVLSGLASEPRTPLSSKARMKRLPKKNQNEKYRLKYLRLRRAAKATVFENA.VCDEIARLEEKFLKAKE
Retrocopy MSVLSGLASEPRTPLSSKARMKRLPKKNQNEKYRLKYLRLRRAAKATVFENA-VCDEIARLEEKFLKAKE

Parental  ERRYLLKKLLQIHALTEGEPQAAAPSHSSSLPLAYGVTSSVGTIQGAGPSTGAEEPFAKKSKKEKKEKGK
          ERRYLLKKLLQIHALTEGEPQAAAPSHSSSLPLAYGVTSSVGTIQGAGPSTGAEEPFAKKSKKEKKEKGK
Retrocopy ERRYLLKKLLQIHALTEGEPQAAAPSHSSSLPLAYGVTSSVGTIQGAGPSTGAEEPFAKKSKKEKKEKGK

Parental  ENSKLEVLKKTSKRKKMEGGARKLVRPIALDPSGQPVFPIGLGGLTVYSLGEIITNRPGFHDENAIYPVG
          ENSKLEVLKKTSKRKKMEG.ARKLVRPIALDPSGQPVFPIGLGGLTVYSLGEIITNRPGFHDENAIYPVG
Retrocopy ENSKLEVLKKTSKRKKMEGNARKLVRPIALDPSGQPVFPIGLGGLTVYSLGEIITNRPGFHDENAIYPVG

Parental  YCSTRVYASMKCPDQKCLYTCQIKDGGVQPQFEIVPEDDPRNTIVGSSADACYEELLRAISAATGKLMPN
          YCSTRVYASMKCPDQKCLYTCQIKDGGVQPQFEIVPEDDPRNTIVGSSADACYEELLRAISAATGKLMPN
Retrocopy YCSTRVYASMKCPDQKCLYTCQIKDGGVQPQFEIVPEDDPRNTIVGSSADACYEELLRAISAATGKLMPN

Parental  PLSCGADFFGFSHPTIHNLIQSCPEAQNCVNYQWVKFDACKPRKGQLSQELPENDAAMSLEAFPTQTFDD
          PLSCGADFFGFSHPTIHNLIQSCPEAQNCVNYQWVKFDACKPRKGQLSQELPENDAAMSLEAFPTQTFDD
Retrocopy PLSCGADFFGFSHPTIHNLIQSCPEAQNCVNYQWVKFDACKPRKGQLSQELPENDAAMSLEAFPTQTFDD

Parental  DHEDSILPGSLDLPELQHEAFVSSYQPEFLTHEPLVDTDLQHLKSPSQCSPIQSSD
          DHEDSILPGSLDLPELQHEAFVSSYQPEFLTHEPLVDTDLQHLKSPSQCSPIQSSD
Retrocopy DHEDSILPGSLDLPELQHEAFVSSYQPEFLTHEPLVDTDLQHLKSPSQCSPIQSSD

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
SRP017611_brain	0.14 RPM	9.56 RPM
SRP017611_kidney	0.14 RPM	15.28 RPM
SRP017611_liver	0.13 RPM	7.60 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1733 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1733 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1733 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000023850	1 retrocopy	retro_rnor_1733 ,