RetrogeneDB ID: retro_rnor_680

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:34098539..34099436(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000050786
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Fam98b
• Ensembl ID: ENSRNOG00000005366
• Aliases: None
• Description: family with sequence similarity 98, member B [Source:MGI Symbol;Acc:MGI:1915465]

Sequence

>retro_rnor_680
ATGAGAGGGCCAGAGCTCGGGCCCGAAACTAGCATGGAGGGGGACGTTCTGGACACCTTGGAGGCGCTGGGGTATAAGGG
TCCACTGTTAGAGGAGCAGGCACTCTCCAAGGCAGCAGAGGGTGGACTGTCTTCTCCTGAGTTTTCGGAGCTTTGCATTT
GGTTAGGCTCCCAGATAAAGTCCTTATGCAACCTGGAAGAAAGCATCACTTCAGCTGGGAGAGATGACCTAGAGGGCTTC
CAGCTTGAGATAAGTGGTTTCTTAAAAGAGATGGCCTGCCCATACTCGGTGCTCGTGTCAGGAGACATTAAAGAGCGCCT
CACGACGAAGGATGACTGCTTGAAACTTCTGTTGTTTTTAAGTACAGAACTGCAAGCTTTACAAATATTACAGAAGAAGA
AACATAAAAATTCTCAGTTAGATAAAAATAGTGAAATTTGCCAGGAAGTTCAAGCTATATGTGATGCTCTTGGGGTCCCC
AAGTCAGACACTTCAGACATTCCACTTCTGCTGAGCCACGTGGAATCAAAGGTGAAGGATATTCTCTCTAAAGTCCAGAA
AAGTCATGTGGGAAAACCATTGCTAAAGGTTGATTTAACTTCTGAACAGGCAGAAAAGCTGGAAAGAATTAATGATGCTC
TTTCCTGTGAATACGAGTGCCGCCGGCGGATGTTAATGAAACGATTGGATGTCACAGTGCAGTCCTTTGGATGGTCCGAT
AGAGCAAAGGCAAAAACAGACAACATAGCAAGAATTTACCAGCCCAAGCGCTATGCTTTGTCACCTAAGACAACAGTCAC
GTTGGCACATCTGCTTGCGGCCCGTGAGGATCTGTCTAAGATCATCAGGACAAGCAGTGGTATCAGTCGGGAGAAGACGG
CATGCGCCATTAATAAG

Alignment

ORF - retro_rnor_680 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 69.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRGPELGPETSMEGDVLDTLEALGYKGPLLEEQALSKAAEGGLSSPEFSELCIWLGSQIKSLCNLEESIT
          MRGPELGPETSMEGDVLDTLEALGYKGPLLEEQALSKAAEGGLSSPEFSELCIWLGSQIKSLCNLEESIT
Retrocopy MRGPELGPETSMEGDVLDTLEALGYKGPLLEEQALSKAAEGGLSSPEFSELCIWLGSQIKSLCNLEESIT

Parental  SAGRDDLEGFQLEISGFLKEMACPYSVLVSGDIKERLTTKDDCLKLLLFLSTELQALQILQKKKHKNSQL
          SAGRDDLEGFQLEISGFLKEMACPYSVLVSGDIKERLTTKDDCLKLLLFLSTELQALQILQKKKHKNSQL
Retrocopy SAGRDDLEGFQLEISGFLKEMACPYSVLVSGDIKERLTTKDDCLKLLLFLSTELQALQILQKKKHKNSQL

Parental  DKNSEICQEVQAICDALGVPKSDTSDIPLLLSHVESKVKDILSKVQKSHVGKPLLKVDLTSEQAEKLERI
          DKNSEICQEVQAICDALGVPKSDTSDIPLLLSHVESKVKDILSKVQKSHVGKPLLKVDLTSEQAEKLERI
Retrocopy DKNSEICQEVQAICDALGVPKSDTSDIPLLLSHVESKVKDILSKVQKSHVGKPLLKVDLTSEQAEKLERI

Parental  NDALSCEYECRRRMLMKRLDVTVQSFGWSDRAKAKTDNIARIYQPKRYALSPKTTVTLAHLLAAREDLSK
          NDALSCEYECRRRMLMKRLDVTVQSFGWSDRAKAKTDNIARIYQPKRYALSPKTTVTLAHLLAAREDLSK
Retrocopy NDALSCEYECRRRMLMKRLDVTVQSFGWSDRAKAKTDNIARIYQPKRYALSPKTTVTLAHLLAAREDLSK

Parental  IIRTSSGISREKTACAINK
          IIRTSSGISREKTACAINK
Retrocopy IIRTSSGISREKTACAINK

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	1.15 RPM	3.67 RPM
SRP017611_kidney	0.98 RPM	1.60 RPM
SRP017611_liver	0.61 RPM	0.94 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_680 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_680 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_680 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000019041	1 retrocopy	retro_etel_211,
Pongo abelii	ENSPPYG00000006336	1 retrocopy	retro_pabe_832,
Rattus norvegicus	ENSRNOG00000005366	1 retrocopy	retro_rnor_680 ,
Rattus norvegicus	ENSRNOG00000030328	1 retrocopy	retro_rnor_614,