RetrogeneDB ID: retro_rnor_1522

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:117434870..117437081(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Senp5
• Ensembl ID: ENSRNOG00000048136
• Aliases: None
• Description: Protein Senp5 [Source:UniProtKB/TrEMBL;Acc:D4A2S8]

Sequence

>retro_rnor_1522
ATGAAAAAACAGAAGAAAATTCTATGGAAGAAAGGAATTCACTTAGCCTTTTCTGAGAAATGGAATGCGGGATATGGAGG
CTTTAAGAAACTCTATTTTCCCCAAAACTTGTGCTTTCTGAAAGCTAAGCTGGGAAGGCCAGTTGTTTGGCATCGGCAGT
CGAAGCATTTCCAGTGTAATAAGAGGGGTCTTCACATCCAGAAAACATGGACCCAGAATGTACCACTTTGTTCAAAGACC
AAGTCTGGAGTGGCCACTCAAAATGTTAGTTCTTTGTATGCCAAAGTGAAAAGAAAGGACACTAAGCACTTCATTTCCTC
CTCCAGGAGTCTCCTGAAACTCCAAGCAGATAAATTACTTTCTTCAGCAAAGAACTTGGGCCGTGAATACTGCAGAGAGA
AAAGCCTTCTGAAGGCAGTTACTGGCTTGCCGGCAAATACTGTTTTAGGTAAGGCCAATGGTCACAAACCTAGCATGGAC
CCACAAGCTTCAGACTTTCCCATGAAGTTCAATGGGGAGAGCCAAAGTCCAAGTGACAGTGGCAAGACTGTGGTTTTGAA
CAAACATAGAAAACGAGTTTGTTATGGCTGCTACCAAGGGCTAGAGCACCACAGGAATAGGAGACCCCTGATTCCAAAAA
AGTTCCAACCTAACCAACATCAAAGAGTCAAAGTGTCTCTTATGATGTATGAGAAACTATCCATGATTAGATTTCGGTAT
AGGATTTTCAGATCCCAGCACTTCAGAACGAAAAGCAGAGTTTGCAAGCTAAGAAAAGCCCAGCGAAGCTGGGTGCAGAA
GGTCACTGGGGACCATCAAGAGAACTTTAGGGATAACAACACTGAGGGTGGCGATTGCAGCCCAGCCCCTTCCCTAGAAC
CTAAAGACCTTTGTCGGTGTCAGCCATACTTTCCAGACATGGACAGTAGTGCTGTGGTGAAGGGAAAAAACTGTCACGTG
CCTGATGGCCACACTAAAGAAAGTCCTGCCTTGGACAAGGAGCATGGTTTAGATGCAGCATTCCCTGACCAGCAGAATGG
CAGCACCACATACACTTGGGACCAGCCATCCTCTTCTCCTAAGTGGGAGTGTACAGAGCAAATTCATGAAATCCCTTTGA
TGGGACATCCTTCTAGTGACAACTTCACTCCGGGAACTGAAAGAGCTCTTATGACTCTGGGGCAGGAAAGCCGGACAAGT
GCTGTCAGCGATGACGGAGTGAAGCTGTCAGTGTCTGGAGCAGACGAATCTGTGAGTAGTGTAGATGGGCCTGTGTCTGA
GGAGCCCGCTCAGAACGAGAACTTCCAGATGGAGGAGGATGGGTCTCTCAGGCAGAACATTCTTAGTTCGAAACTGCTGG
ACCACCCTTACTGTAAGAGTCCACTGGATGCTCCCTTGGTGTGCAGTGAGCTCAAAGTAGAAAACCAAGTGGCAGGTGGC
AAGAGTGGCCAGACAGCGTCTCCCGTGGATGATGAGCAGCTCTCGACCTGCCTTTCTGGGTTCCTAGACGAGGTTATGAA
AAAGTATGGAAGTCTGGTCCCACTCAGTGAGAAAGATGTCCTTGGGAGATTAAAAGATGTCTTTAATGAAGACTTTTCTA
ATAGAAAACCATTTATCAATAGGGAAATAACAAACTACCGGGTCAGACATCAAAAGTGTAACTTCTGAATCTTCTACAAC
AAGCACATGCTGGATATGGACGACCTGGCAACTTTGGATGGTCAGAATTGGTTGAATGACCAGGTTATTAATATGTATGG
CGAGCTGATAATGGACGCAGTCCCCGACAAGGTCCACTTCTTCAACAGCTTTTTCCATAGACAGCTGGTAACCAAAGGCT
ATAATGGAGTTAAGAGATGGACTAAGAAGGTGGATTTGTTTAAAAAGAGTCTTCTGTTGATTCCCATCCACCTGGAGGTC
CACTGGTCTCTCATTACTGTGACACTCTCCAGTCGGATTATTTCATTTTATGATTCCCAAGGCATTCATTTTAAATTTTG
TGTAGAGAATATAAGAAAGTATTTGCTGACTGAAGCCAGAGAAAAAAATAGACCTGAATTTCTTCAGGGTTGGCAGACTG
CTGTTACAAAGTGTATTCCACAACAGAAAAATGACAGTGACTGTGGAGTCTTTGTGCTCCAGTACTGCAAGTGCCTCGCC
CTAGAGCAGCCTTTCCAGTTTTCTCAAGAAGACATGCCTCGTGCGGAAGAG

Alignment

ORF - retro_rnor_1522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.24 %
• Parental protein coverage: 98.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKKQKKILWKKGIHLAFSEKWNAGFGGFKKLYFPQNLCFLKAKLGRPVVWHRQSKHFQCNKRGLHIQKTW
          MKKQKKILWKKGIHLAFSEKWNAG.GGFKKLYFPQNLCFLKAKLGRPVVWHRQSKHFQCNKRGLHIQKTW
Retrocopy MKKQKKILWKKGIHLAFSEKWNAGYGGFKKLYFPQNLCFLKAKLGRPVVWHRQSKHFQCNKRGLHIQKTW

Parental  TQDVPLCSKTKSGVATQNVSSLYAKVKRKDTKHFISSSRSLLKLQADKLLSSAKNLGREYCREKSLLKAV
          TQ.VPLCSKTKSGVATQNVSSLYAKVKRKDTKHFISSSRSLLKLQADKLLSSAKNLGREYCREKSLLKAV
Retrocopy TQNVPLCSKTKSGVATQNVSSLYAKVKRKDTKHFISSSRSLLKLQADKLLSSAKNLGREYCREKSLLKAV

Parental  TGLSANTVLGKANGHKPSTDPQASDFPMKFNGESQSPSDSGKTVVLNKHRKRVCYGCYQGLEHHRNRRPL
          TGL.ANTVLGKANGHKPS.DPQASDFPMKFNGESQSPSDSGKTVVLNKHRKRVCYGCYQGLEHHRNRRPL
Retrocopy TGLPANTVLGKANGHKPSMDPQASDFPMKFNGESQSPSDSGKTVVLNKHRKRVCYGCYQGLEHHRNRRPL

Parental  IPKKFQPNQHRRVKVSLMMYEKLSMIRFRYRIFRSQHFRTKSRVCKLRKAQRSWVQKVTGDHQENFRDNN
          IPKKFQPNQH.RVKVSLMMYEKLSMIRFRYRIFRSQHFRTKSRVCKLRKAQRSWVQKVTGDHQENFRDNN
Retrocopy IPKKFQPNQHQRVKVSLMMYEKLSMIRFRYRIFRSQHFRTKSRVCKLRKAQRSWVQKVTGDHQENFRDNN

Parental  TEGGDCSPVPSLEPKDPCRCQPYFPDMDSSAVVKGKNCHVPDGHTKESPALDKEHGLDAAFPDQQNGSTT
          TEGGDCSP.PSLEPKD.CRCQPYFPDMDSSAVVKGKNCHVPDGHTKESPALDKEHGLDAAFPDQQNGSTT
Retrocopy TEGGDCSPAPSLEPKDLCRCQPYFPDMDSSAVVKGKNCHVPDGHTKESPALDKEHGLDAAFPDQQNGSTT

Parental  YTWDQPSSSPKWECTEQIHEIPLMGHPSSDNFTPGTERALMTLGQESGTSAVSDDGVKLSVSGADESVSS
          YTWDQPSSSPKWECTEQIHEIPLMGHPSSDNFTPGTERALMTLGQES.TSAVSDDGVKLSVSGADESVSS
Retrocopy YTWDQPSSSPKWECTEQIHEIPLMGHPSSDNFTPGTERALMTLGQESRTSAVSDDGVKLSVSGADESVSS

Parental  VDGPVSEEPAQNENFQMEEDGSLRQNILSSKLLDHPYCKSPLDAPLVCSELKVENQVAGGKSGQTASPVD
          VDGPVSEEPAQNENFQMEEDGSLRQNILSSKLLDHPYCKSPLDAPLVCSELKVENQVAGGKSGQTASPVD
Retrocopy VDGPVSEEPAQNENFQMEEDGSLRQNILSSKLLDHPYCKSPLDAPLVCSELKVENQVAGGKSGQTASPVD

Parental  DEQLSTCLSGFLDEVMKKYGSLVPLSEKDVLGRLKDVFNEDFSNRKPFINREITNYRARHQKCNFRIFYN
          DEQLSTCLSGFLDEVMKKYGSLVPLSEKDVLGRLKDVFNEDFSNRKPFINREITNYR.RHQKCNF.IFYN
Retrocopy DEQLSTCLSGFLDEVMKKYGSLVPLSEKDVLGRLKDVFNEDFSNRKPFINREITNYRVRHQKCNF*IFYN

Parental  KHMLDMDDLATLDGQNWLNDQVINMYGELIMDAVPDKVHFFNSFFHRQLVTKGYNGVKRWTKKVDLFKKS
          KHMLDMDDLATLDGQNWLNDQVINMYGELIMDAVPDKVHFFNSFFHRQLVTKGYNGVKRWTKKVDLFKKS
Retrocopy KHMLDMDDLATLDGQNWLNDQVINMYGELIMDAVPDKVHFFNSFFHRQLVTKGYNGVKRWTKKVDLFKKS

Parental  LLLIPIHLEVHWSLITVTLSSRIISFYDSQGIHFKFCVENIRKYLLTEAREKNRPEFLQGWQTAVTKCIP
          LLLIPIHLEVHWSLITVTLSSRIISFYDSQGIHFKFCVENIRKYLLTEAREKNRPEFLQGWQTAVTKCIP
Retrocopy LLLIPIHLEVHWSLITVTLSSRIISFYDSQGIHFKFCVENIRKYLLTEAREKNRPEFLQGWQTAVTKCIP

Parental  QQKNDSDCGVFVLQYCKCLALEQPFQFSQEDMPRVRK
          QQKNDSDCGVFVLQYCKCLALEQPFQFSQEDMPR...
Retrocopy QQKNDSDCGVFVLQYCKCLALEQPFQFSQEDMPRAEE

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	0.00 RPM	1.29 RPM
SRP017611_kidney	0.00 RPM	0.35 RPM
SRP017611_liver	0.07 RPM	0.47 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1522 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1522 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1522 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000001773	1 retrocopy	retro_rnor_1568,
Rattus norvegicus	ENSRNOG00000048136	2 retrocopies	retro_rnor_1522 , retro_rnor_531,
Tursiops truncatus	ENSTTRG00000013899	1 retrocopy	retro_ttru_1914,