RetrogeneDB ID: retro_rnor_1953

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:17879420..17882516(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Scaf11
• Ensembl ID: ENSRNOG00000005263
• Aliases: Scaf11, Sfrs2ip, Srsf2ip
• Description: SFRS2-interacting protein [Source:RefSeq peptide;Acc:NP_001258099]

Sequence

>retro_rnor_1953
ATGAAGAAGAAACCCGTATATAATCAGAGTGTGGGTGATCAGGAGAGTGAAGATGCGGAAGGTGAAGAAAACAGAAATAA
TGCTGATACTTCCGGCTTACTGTACAGTGAGGTGGACAGATGTCCAATCTGTCTTAGTTGCCTATTAGGGAAGGAAGTTG
GTTTTCCAGAAAGTTGTAATCATGTCTTCTGTATGGCCTGTATTCTTAAATGGGCAGAGATACTGGCTTCTTGTCCAATC
GATCGGAAACCCTTTCAGGCAGTGTTTGAACTCCGTGCATTTGAAGGTTGTGCTAAGATTCAGGTAAAAAGACGGTCGAG
AGAATTAGACGACAAGGAAAATGAGGAGTCTTTTAAGAAACAGCTCGTTTATCATGAAAGTTCCAAAAGCGACAGGAGAA
AAGGAAACACTGTAAGAGAAGATCTGTTATGTGAGAGATCTGATGACTTGAAGGTGTTGTATAGAAACTTTTCAAACAAT
AAAATGGGTGGAAAGAAAAATGCTACAGTAAAGACAAACAAGGTTCAAAGATTGAATCAGTGTACAGATTCTTGTGTGAG
AAGTGACATGCCCAGTGTATCTTCATGTGACGGCCACAGTTGGGGACCTCGCACCTACAGAGTTTCCTGTACAGAATCTA
TAGAAGTCAATGAAATCAATGCATTGATTAGGCAGAAACGACAGGAACTGGAGTTGTCATGGTTTCCTAATACATTACCT
GGGAATGGAAGAGTTGGCTCTGTACCCTGGAGTGTGGAGACAGCAGTTCTTCCTCTGGTTTCCTCAGTGCTGCCAAGGAC
GATTTTTCCAGCAAGTACCATGTCACTAGAAAATTTTGGTACTTCTCATAAGGGGTATGCACTAGCACATACCCAAGGAG
GAGGAGAAAAAAAGCAAACTTCAGGTACATCAAACACCAGAGGATCAAGATGAAAACCTGCAACAACTGCTCCTACAAGG
AGGTCCACAGGAAACACACGTGTTGAGACAGTCAGTCCATCCCAGAAGTCCCCAGTGCCAAACTACTCTGAGTGTGATGC
CCCAGGGAATAGTAATTCCTCTGTCAGTATTTCCCCTCCAGCTGAATCAGAAAAGCAAACAAGACAGGCTCCAAAACGGA
AGTCAGTAAGGAGAGGAAGAAAACCACCTTCTTTGAAAAAGAAACCTCTGAAATCTGTACCTCCTGCTGAAAAAACCACA
TCTAGCGATTCAGTAGAGGAAGACACTGTGGATTCTGACACTCCACCCGTGTTGGAAAAGGAGCAGCAATCATGTGTAGA
GAGTAGTAGCATTTGCTCTATTCAGACAGATGAAGAGAATCATTTGGCTAAGTGCTTGGAAAGTTGCGATGAACAAACAG
AAGAAAATGAACAAACCAAGAATCATGAGATCGAGGAACAAACAGAAATTTTAAATTCTGAATCTTGCACTCAGTATCCT
CCTGTGCTTGTTGGAGAGGATTCAGGGATAGAGACTAAGGAGTTATGTGTAGACAATGATGTTTCTACAGATTATTCTCT
AAAAGGAAGTGATCCATTGGAAAATCAAGAACAGGACTCTGGAAGCTCAGGGTCAGAGGTGCAGGCATCCGTGTGTACGG
AGAGTCTGCCTGAGGATTTCCTTACGTGTCCACCGTCTGACATTGAAGGACACCAGCCAGTGTCCGGTCCCCTGGGTGAA
GTATCTGAAAACGCCACCCCAGTGCTTAGTGATGAAAGAGCAGAGGACAGTCTCATGGTAGGAAATGCTGATTTGAATGA
TTCTGTAGAGAACACAGAAGCATTTGTAATGAGCCCCAAAGTGGAGTCTTCTGAGGGTGAAATTACACATGGACTGAACA
GACATTGTATTCCCAGCTCAGACACGGAGTTGCCTGAGCTTATTCAAACAGAAAATACAGAAATAATTCCAACATGTGGC
ACTTTAGAAAATGAAAGTTCTGGTGCTGTTCAAGGTTGTGAAGATACCTTACTAAAACATAATCTTGACAACACCCAATT
GGATAACTCCTTAGAAGAAAAGACAGACTCTCTGGTTGAGCATCCCATCCATGCAGAGTTACCTCACGAAGAAGTTGAAC
AGAGTGAGAAACATTTCAGTGAAGATAATAATGAAATAGTACCTATGGAGTGCGATTCTTTCTGTAGTGACCAGAATGAG
TCTGAAGTAGAGTCATCAGCAAATACTGACCCCAAACAGTTGAGTGAAAATTCTGTGACACACAGTTCTGACAACAAGCT
GTCTTCTGATCCTGTAGTTGAGAATGTTGAAACTGTAGCTCAACCAGCTGAAAGCCTAGTGGATAAAGCCCCAAAGCCTC
GAACTCGGAGATCTAGATTCCATTCTCCGTCTACAACTTGGTCTCCCAACAAAGATGCTGCACAAGAAAAGAGGCGCGCT
CAGTCTCCATCTCCGAAAAGAGAGACTGCAGTAGAAAGTAAGAGTTCTCAGTCACCATCCCCCAAGAGAGAGTCTGCCAG
AGGACGAAGAAAATCCCATTCTCTCTCACCAAAAAAAGATGTATCAAGAGAAAGGAGGCAGTCTCGGTCTCCAAAGAGAG
AGAATGCTAGGGAAGCTAAAAGGTCTGAGTCAGGCTCCCCAAGAAGAGACACTTCTAGAGAGAACCAGAGGTCTCAGTCC
AGGGTGAAAGATTCTTCCTCCAGAGAAAAATCTAGGTCCCGGAGCAGAGAAAGAGAGAGTGACAGAGATGCTCAGAGGAG
AGATCGAGATAGAGAGAGGCGAGCCAGAAGGTGGTCCCGGTCTAGATCTTGCTCTCGATCGCCATCAAGATCAAGAACGA
AGAGTAAGAGTTCATCATTTGGTAGAAACGAAAGAGATACTTACTCTCCCCGGTGGAGGGAAAAATGGACAAATGATGGT
TGGAGGTGTCCCAGAGGGAACGACCGGTACCGGAGGAATGATTCAGAGAAACAGAATGAAAACACAAGAAATGAAAAAGA
TGATATCACTGCAGATAATACTAATGATCCCAGTTCCACAGATAAGCATAGAGATGACTGTCCCAGCTGGGTGACAGAAA
AAATAAACTCTGGGCCAGATCCAAGGACCAGAAATCCAGAAAAGTTAAAAGATTCC

Alignment

ORF - retro_rnor_1953 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.9 %
• Parental protein coverage: 72.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKKKPVYNQSVGDQESEDAEGEENRNNADTSGLLYSEVDRCPICLSCLLGKEVGFPESCNHVFCMACILK
          MKKKPVYNQSVGDQESEDAEGEENRNNADTSGLLYSEVDRCPICLSCLLGKEVGFPESCNHVFCMACILK
Retrocopy MKKKPVYNQSVGDQESEDAEGEENRNNADTSGLLYSEVDRCPICLSCLLGKEVGFPESCNHVFCMACILK

Parental  WAEILASCPIDRKPFQAVFELRAFEGCAKIQVKRRSRELDDKENEESFKKQLVYHESSKSDKRKGNTVRE
          WAEILASCPIDRKPFQAVFELRAFEGCAKIQVKRRSRELDDKENEESFKKQLVYHESSKSD.RKGNTVRE
Retrocopy WAEILASCPIDRKPFQAVFELRAFEGCAKIQVKRRSRELDDKENEESFKKQLVYHESSKSDRRKGNTVRE

Parental  DLLCERSDDLKVLYRNFSNNKMGGKKNATVKTNKVQRLNQCTDSCVRSDMPSVSSCDGHSWGPRTYRVSC
          DLLCERSDDLKVLYRNFSNNKMGGKKNATVKTNKVQRLNQCTDSCVRSDMPSVSSCDGHSWGPRTYRVSC
Retrocopy DLLCERSDDLKVLYRNFSNNKMGGKKNATVKTNKVQRLNQCTDSCVRSDMPSVSSCDGHSWGPRTYRVSC

Parental  TESIEVNEINALIRQKRQELELSWFPNTLPGNGRVGSVPWSVETAVLPLVSSVLPRTIFPASTMSLENFG
          TESIEVNEINALIRQKRQELELSWFPNTLPGNGRVGSVPWSVETAVLPLVSSVLPRTIFPASTMSLENFG
Retrocopy TESIEVNEINALIRQKRQELELSWFPNTLPGNGRVGSVPWSVETAVLPLVSSVLPRTIFPASTMSLENFG

Parental  TSHKGYALAHTQGGGEKKQTSGTSNTRGSRRKPATTAPTRRSTRNTRVETVSPSQKSPVPNYSECDAPGN
          TSHKGYALAHTQGGGEKKQTSGTSNTRGSR.KPATTAPTRRST.NTRVETVSPSQKSPVPNYSECDAPGN
Retrocopy TSHKGYALAHTQGGGEKKQTSGTSNTRGSR*KPATTAPTRRSTGNTRVETVSPSQKSPVPNYSECDAPGN

Parental  SNSSVSISPPAESEKQTRQAPKRKSVRRGRKPPSLKKKPRKSLPPAEKTTSSDSVEEDTVDSDTPPVLEK
          SNSSVSISPPAESEKQTRQAPKRKSVRRGRKPPSLKKKP.KS.PPAEKTTSSDSVEEDTVDSDTPPVLEK
Retrocopy SNSSVSISPPAESEKQTRQAPKRKSVRRGRKPPSLKKKPLKSVPPAEKTTSSDSVEEDTVDSDTPPVLEK

Parental  EQQSCVESSSICSIQTDEENHLAKCLESCDEQTEENEQTKNHEIEEQTEILNSESCTQYPPVLVGEDSGI
          EQQSCVESSSICSIQTDEENHLAKCLESCDEQTEENEQTKNHEIEEQTEILNSESCTQYPPVLVGEDSGI
Retrocopy EQQSCVESSSICSIQTDEENHLAKCLESCDEQTEENEQTKNHEIEEQTEILNSESCTQYPPVLVGEDSGI

Parental  EAKELCVDNDVSTDSSLKGSDPLENQEQGSGSSGSEVQASVCTESPPEDFLTCPPSDIEGHQPVSGPLGE
          E.KELCVDNDVSTD.SLKGSDPLENQEQ.SGSSGSEVQASVCTES.PEDFLTCPPSDIEGHQPVSGPLGE
Retrocopy ETKELCVDNDVSTDYSLKGSDPLENQEQDSGSSGSEVQASVCTESLPEDFLTCPPSDIEGHQPVSGPLGE

Parental  VSENATPVLSDERAEDSLMVGNADLNDSVENTEAFVMSPKVESSEGEITHGLNRHCIPSSDTELPELIQT
          VSENATPVLSDERAEDSLMVGNADLNDSVENTEAFVMSPKVESSEGEITHGLNRHCIPSSDTELPELIQT
Retrocopy VSENATPVLSDERAEDSLMVGNADLNDSVENTEAFVMSPKVESSEGEITHGLNRHCIPSSDTELPELIQT

Parental  ENTEIIPTCGTLENESSGAVQGCEDTLLKHNLDNTQLDNSLEEKTDSLVEHPIHAELPHKEVEQSEKHFS
          ENTEIIPTCGTLENESSGAVQGCEDTLLKHNLDNTQLDNSLEEKTDSLVEHPIHAELPH.EVEQSEKHFS
Retrocopy ENTEIIPTCGTLENESSGAVQGCEDTLLKHNLDNTQLDNSLEEKTDSLVEHPIHAELPHEEVEQSEKHFS

Parental  EDNNETVPMECDSFCSDQNESEVESSANTDPKQLSENSVTHSSDNKLSSDPVVENVETVAQPAESLVDKA
          EDNNE.VPMECDSFCSDQNESEVESSANTDPKQLSENSVTHSSDNKLSSDPVVENVETVAQPAESLVDKA
Retrocopy EDNNEIVPMECDSFCSDQNESEVESSANTDPKQLSENSVTHSSDNKLSSDPVVENVETVAQPAESLVDKA

Parental  PKPRTRRSRFHSPSTTWSPNKDAAQEKRRAQSPSPKRETAVESKSSQSPSPKRESARGRRKSRSLSPKKD
          PKPRTRRSRFHSPSTTWSPNKDAAQEKRRAQSPSPKRETAVESKSSQSPSPKRESARGRRKS.SLSPKKD
Retrocopy PKPRTRRSRFHSPSTTWSPNKDAAQEKRRAQSPSPKRETAVESKSSQSPSPKRESARGRRKSHSLSPKKD

Parental  VSRERRQSRSPKRENAREAKRSESGSPRRDTSRENQRSQSRVKDSSSREKSRSRSRERESDRDAQRRDRD
          VSRERRQSRSPKRENAREAKRSESGSPRRDTSRENQRSQSRVKDSSSREKSRS.................
Retrocopy VSRERRQSRSPKRENAREAKRSESGSPRRDTSRENQRSQSRVKDSSSREKSRSXXXXXXXXXXXXXXXXX

Parental  RERRARRWSRSRSRSRSPSRSRTKSKSSSFGRNERDTYSPRWREKWTNDGWRCPRGNDRYRRNDSEKQNE
          ..RRARRWSRSRS.SRSPSRSRTKSKSSSFGRNERDTYSPRWREKWTNDGWRCPRGNDRYRRNDSEKQNE
Retrocopy XXRRARRWSRSRSCSRSPSRSRTKSKSSSFGRNERDTYSPRWREKWTNDGWRCPRGNDRYRRNDSEKQNE

Parental  NTRNEKDDITADNTNDPSSTDKHRDDCPSWVTEKINSGPDPRTRNPEKLKDS
          NTRNEKDDITADNTNDPSSTDKHRDDCPSWVTEKINSGPDPRTRNPEKLKDS
Retrocopy NTRNEKDDITADNTNDPSSTDKHRDDCPSWVTEKINSGPDPRTRNPEKLKDS

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	22.79 RPM
SRP017611_kidney	0.56 RPM	71.11 RPM
SRP017611_liver	0.07 RPM	26.16 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1953 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1953 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1953 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	ENSRNOG00000005263	1 retrocopy	retro_rnor_1953 ,