RetrogeneDB ID: retro_rnor_2345

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:28249276..28251346(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000040045
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Crnkl1
• Ensembl ID: ENSRNOG00000010587
• Aliases: None
• Description: Crooked neck-like protein 1 [Source:UniProtKB/Swiss-Prot;Acc:P63155]

Sequence

>retro_rnor_2345
ATGGCGGCTTCCACGGCAGCCGGGAAACAGCGGATTCCTAAAGTGGCCAAGGTGAAGAACAAAGCGCCAGCAGAGGTGCA
GATAACCGCAGAGCAGCTCTTAAGGGAGGCTAAAGAAAGAGAGCTCGAGCTCCTCCCACCCCCACCTCAGCAGAAGATCA
CAGACGAGGAAGAACTAAACGATTACAAACTACGGAAAAGGAAGACTTTCGAAGATAATATAAGAAAAAACAGAACTGTG
ATTAGCAACTGGATCAAATACGCACAATGGGAGGAAAGTCTGAAGGAAATTCAAAGGGCCCGATCCATATACGAGCGTGC
TTTAGATGTCGACTACCGAAATATCACACTCTGGCTGAAATATGCAGAAATGGAAATGAAGAACCGCCAGGTCAACCATG
CCCGAAATATCTGGGACCGTGCCATAACAACCCTGCCGCGAGTCAACCAGTTCTGGTACAAATACACGTACATGGAGGAG
ATGCTGGGCAATGTTGCCGGTGCTCGTCAGGTGTTTGAGCACTGGATGGAATGGCAGCCTGAGGAGCAGGCCTGGCACTC
CTACATCAACTTCGAGCTGAGATACAAAGAGGTGGAGCGGGCCCGCACCATTTATGAACGCTTTGTGCTCGTGCACCCTG
CTGTGAAGAACTGGATCAAGTACGCTCGATTTGAAGAGAAGCATGCGTATTTTGCCCATGCGCGGAAAGTCTACGAGAGA
GCAGTTGAGTTTTTTGGGGATGAGCATATGGACGAACACCTCTATGTGGCCTTTGCTAAATTTGAAGAAAATCAAAAAGA
ATTTGAAAGGGTACGAGTTATCTACAAATATGCCCTGGATAGGATTTCCAAGCAAGAGGCCCAAGAGCTCTTTAAAAACT
ATACCATCTTTGAGAAGAAGTTTGGTGACCGGAGGGGTATAGAAGACATCATCGTGAGCAAACGGAGATTCCAGTATGAA
GAAGAAGTGAAGGCTAATCCACACAATTATGATGCATGGTTTGATTATTTACGCTTGGTGGAAAGTGATGCAGAAGCGGA
CACTGTGCGGGAAGTCTATGAGCGAGCCATTGCCAATGTGCCACCCATCCAGGAGAAGAGGCACTGGAAACGCTACATCT
ACCTCTGGGTTAACTACGCACTCTATGAAGAGCTGGAGGCCAAGGATCCTGAGAGGACAAGACAGGTGTATCAAGCATCT
TTGGAACTAATTCCTCACAAAAAGTTCACGTTTGCCAAAATGTGGTTATATTACGCACAGTTTGAAATAAGACAGAAAAA
TCTGCCATTTGCCAGAAGAGCTTTGGGAACTTCCATAGGCAAATGTCCCAAGAACAAGTTATTCAAAGGTTACATAGAAC
TGGAACTGCAGCTTCGAGAATTTGACAGATGCAGGAAGCTTTACGAAAAGTTTTTGGAATTTGAACCTGAAAATTGTACC
TCGTGGATTAAGTTTGCAGAATTAGAGACAATCCTTGGTGATATTGAGAGAGCTCGGGCAATCTATGAATTAGCCATCAG
CCAGCCACGCTTGGATATGCCAGAGGTACTTTGGAAATCATATATTGATTTTGAGATTGAGCAGGAAGAAACTGAGAGAA
CACGAAATCTTTACCGACAGTTGCTTCAGCGAACACAGCACGTCAAGGTATGGATCAGTTTTGCTCAGTTTGAATTATCT
TCTGTGAAAGAAGGAAGTGTGGCTAAATGCAGACAGATTTATGAAGAAGCTAACAAAACCATGAGAAACTGTGAAGAAAA
AGAAGAGAGGCTTATGTTGCTGGAGTCCTGGCGAAGTTTCGAAGATGAATTTGGAACAGTATCAGACAAGGAGAGAGTAG
ACAAACTCATGCCAGAAAAGGTCAAGAAGAGAAGAAAGGTCCAGGCTGACGATGGGTCTGATGCCGGATGGGAAGAGTAC
TATGACTACATCTTTCCAGAAGATGCTGCCAACCAGCCTAACCTCAAGCTGCTGGCGATGGCCAAGCTTTGGAAGAAACA
GCAACAAGAAAGAGAAGCTGCCGAACAGGATCCAGATAAGGACATTGATGAGAGTGAATCCTCATCTTTT

Alignment

ORF - retro_rnor_2345 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASTAAGKQRIPKVAKVKNKAPAEVQITAEQLLREAKERELELLPPPPQQKITDEEELNDYKLRKRKTF
          MAASTAAGKQRIPKVAKVKNKAPAEVQITAEQLLREAKERELELLPPPPQQKITDEEELNDYKLRKRKTF
Retrocopy MAASTAAGKQRIPKVAKVKNKAPAEVQITAEQLLREAKERELELLPPPPQQKITDEEELNDYKLRKRKTF

Parental  EDNIRKNRTVISNWIKYAQWEESLKEIQRARSIYERALDVDYRNITLWLKYAEMEMKNRQVNHARNIWDR
          EDNIRKNRTVISNWIKYAQWEESLKEIQRARSIYERALDVDYRNITLWLKYAEMEMKNRQVNHARNIWDR
Retrocopy EDNIRKNRTVISNWIKYAQWEESLKEIQRARSIYERALDVDYRNITLWLKYAEMEMKNRQVNHARNIWDR

Parental  AITTLPRVNQFWYKYTYMEEMLGNVAGARQVFERWMEWQPEEQAWHSYINFELRYKEVERARTIYERFVL
          AITTLPRVNQFWYKYTYMEEMLGNVAGARQVFE.WMEWQPEEQAWHSYINFELRYKEVERARTIYERFVL
Retrocopy AITTLPRVNQFWYKYTYMEEMLGNVAGARQVFEHWMEWQPEEQAWHSYINFELRYKEVERARTIYERFVL

Parental  VHPAVKNWIKYARFEEKHAYFAHARKVYERAVEFFGDEHMDEHLYVAFAKFEENQKEFERVRVIYKYALD
          VHPAVKNWIKYARFEEKHAYFAHARKVYERAVEFFGDEHMDEHLYVAFAKFEENQKEFERVRVIYKYALD
Retrocopy VHPAVKNWIKYARFEEKHAYFAHARKVYERAVEFFGDEHMDEHLYVAFAKFEENQKEFERVRVIYKYALD

Parental  RISKQEAQELFKNYTIFEKKFGDRRGIEDIIVSKRRFQYEEEVKANPHNYDAWFDYLRLVESDAEADTVR
          RISKQEAQELFKNYTIFEKKFGDRRGIEDIIVSKRRFQYEEEVKANPHNYDAWFDYLRLVESDAEADTVR
Retrocopy RISKQEAQELFKNYTIFEKKFGDRRGIEDIIVSKRRFQYEEEVKANPHNYDAWFDYLRLVESDAEADTVR

Parental  EVYERAIANVPPIQEKRHWKRYIYLWVNYALYEELEAKDPERTRQVYQASLELIPHKKFTFAKMWLYYAQ
          EVYERAIANVPPIQEKRHWKRYIYLWVNYALYEELEAKDPERTRQVYQASLELIPHKKFTFAKMWLYYAQ
Retrocopy EVYERAIANVPPIQEKRHWKRYIYLWVNYALYEELEAKDPERTRQVYQASLELIPHKKFTFAKMWLYYAQ

Parental  FEIRQKNLPFARRALGTSIGKCPKNKLFKGYIELELQLREFDRCRKLYEKFLEFGPENCTSWIKFAELET
          FEIRQKNLPFARRALGTSIGKCPKNKLFKGYIELELQLREFDRCRKLYEKFLEF.PENCTSWIKFAELET
Retrocopy FEIRQKNLPFARRALGTSIGKCPKNKLFKGYIELELQLREFDRCRKLYEKFLEFEPENCTSWIKFAELET

Parental  ILGDIERARAIYELAISQPRLDMPEVLWKSYIDFEIEQEETERTRNLYRQLLQRTQHVKVWISFAQFELS
          ILGDIERARAIYELAISQPRLDMPEVLWKSYIDFEIEQEETERTRNLYRQLLQRTQHVKVWISFAQFELS
Retrocopy ILGDIERARAIYELAISQPRLDMPEVLWKSYIDFEIEQEETERTRNLYRQLLQRTQHVKVWISFAQFELS

Parental  SGKEGSVAKCRQIYEEANKTMRNCEEKEERLMLLESWRSFEDEFGTVSDKERVDKLMPEKVKKRRKVQAD
          S.KEGSVAKCRQIYEEANKTMRNCEEKEERLMLLESWRSFEDEFGTVSDKERVDKLMPEKVKKRRKVQAD
Retrocopy SVKEGSVAKCRQIYEEANKTMRNCEEKEERLMLLESWRSFEDEFGTVSDKERVDKLMPEKVKKRRKVQAD

Parental  DGSDAGWEEYYDYIFPEDAANQPNLKLLAMAKLWKKQQQEREAAEQDPDKDIDESESSSF
          DGSDAGWEEYYDYIFPEDAANQPNLKLLAMAKLWKKQQQEREAAEQDPDKDIDESESSSF
Retrocopy DGSDAGWEEYYDYIFPEDAANQPNLKLLAMAKLWKKQQQEREAAEQDPDKDIDESESSSF

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	0.65 RPM	6.25 RPM
SRP017611_kidney	1.19 RPM	6.77 RPM
SRP017611_liver	0.61 RPM	3.63 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2345 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2345 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2345 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
Macropus eugenii	ENSMEUG00000012167	1 retrocopy	retro_meug_44,
Myotis lucifugus	ENSMLUG00000016513	1 retrocopy	retro_mluc_1434,
Mus musculus	ENSMUSG00000001767	1 retrocopy	retro_mmus_207,
Rattus norvegicus	ENSRNOG00000010587	1 retrocopy	retro_rnor_2345 ,