RetrogeneDB ID: retro_rnor_2064

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:142628174..142630096(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fgfr1
• Ensembl ID: ENSRNOG00000016050
• Aliases: None
• Description: fibroblast growth factor receptor 1 precursor [Source:RefSeq peptide;Acc:NP_077060]

Sequence

>retro_rnor_2064
CTGCTACAGCTTCACTGTCGGCTGCGCAATGATGTGCAGAGCATCAACTCGCTGTGGGTGCAGCTGGTGGAGAGCAGTCG
CACCCACATCACAGGGGAGGAGGTGGAGGTGCAGGATTCCATCCCCGCTGACTCTGGCCTCTACGCTTGTGTGACCAGCA
GCCCCTCTGGTAGCGATACCACCTACTTCTCCGCCAATGTCTCAGATGCACTGCCATCCTCGGAGGATGATGATGACGAC
GATGATTCCTCCTCAGAGGAGAAAGGGACAGACACCACCAAACCAAACCATAGGCCTGTAGCGCCATACTGGACATCCCC
AGAAAAAATGGAGAGGAAACTGCACGCAGTGCCAGCTGCCAAGACGGTGAAGTTCAAATGCCCGTCGAGCGGGACACCCA
GCCCCACTTTGCGCTGGTTGAAGAATGGCAAGGAATTCAAACCTGACCACTGAATTGGAGGCTACAAGGTTCATTATGCC
ACTTGGAGCATCATAGTGGACTCTGTGGTGCCTTTCAACAAGGGCAACTACACCTGCACCATGGAGAATGAGTATGGGAG
CATTAACCACACCTACCAGCTAGATGTTGTGGAGCGATCCCCTCACCGGCCCATCCTTCAGGCAGGGCTACCTGCCAACA
AGACCGTGGCCCCGGGCAGCACCGTGGAGTTCATGTGTAAGGTGTACAGTGACCCACAGCCTCACATCCAGTGGCTGAAG
CACATCAAGATGAACGGGAGTAAGATTGGTCCAGACAGCTTGCCATATGTCCAGATCCTGAAGACTGCTGGAGTTAATAC
CACCGACAAGGAAATGGAGGTGCTTCATCTACGGAATGTCTCCTTTGAGGATGCAGGAGGGTATACGTGCTTGGCAGGTA
ACTCTATTGGACTCTCCCATCACTCTACATGGTTGACCGTTGGGAAGCCCTGGAAGAGAGACAAGCCATGATGACCTCAC
CTCTGTACCTGGAAATCATTATCTATTGCACCGGGGCCTTCCTGATCTCCTGTATGCTGGGGCCCGTCGTCATCTACAAG
ATGAAAAGCGGCATCAAGAAGAGCGACTTCCATAGCCAGATGGCTGTGCATAAACTGGCTAAGAGCACCCTTCTGTGCAG
ACAGGTAACAGTGTCAGCTGACTCTAGTGCATCCATGAACTCTGGGGTTCACCTGGTTTAGCCTTCATAACTCTCCTCCA
GTGGGACCCCCCATGCTAGCTGGTGTCTCTGAATATGACCTCCCTGAAGATCCCTGCTGGGAGCTGCCCCGAGACAGACT
GGTCTTAAGAAAACCGCTTGGCAAGGGCTTCGGGCAGGTGGTATTGGCCGAAGCCATCGGTCTGGATAAGGACAAACCCA
ACCGCATGACCAAAGTGGCGGAGAAAGATGTTGAAGTCTAATGAAACAGAGAAGGACCTGTCAGACCTGATCTCAGAGAT
GGAGATGATGAAAATGATCGGGAAGCACAAGAATATCATTAATCTGCTGGGGGTGTGCACCCAGGATGATTCCCTCTATG
TCATCGTGGATTATGCCCCCAAAGGCAATCTTTGGGAGTATCTGCAGGCCCGGAGGCCTCCTGGGCTGGAGTAGTGCTAC
AGCCCCAGCCACAACCCCGAGGAACAGCTGTCTTCCAAAGATCTGGTGTCCTGTGCCTATCAAGTGGTCTGGGGCATGGA
GTATCTTGCCTCAAAGAAGTTTATACACTGAGACCTGGCTGCTAGGAATGTCCTGGTGACAGAGGATAAGGTCATGATGA
TCGCAGACTTTGGCCTAGCTCGAGACATTCACCATATCGACTACTATAAGAAAACCACCAACGTGGCTGCCTGTGAAGTG
GATGGCACCTGAGGCATTGTTTGACCGGATCTACATCCCAGAAGGATGGGTGGTCTTTTGGGGTGCTCTTGTGGGAGATC
TT

Alignment

ORF - retro_rnor_2064 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.27 %
• Parental protein coverage: 78.35 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LLQLRCRLRDDVQSINWLRDGVQLAESNRTRITGEEVEVRDSIPADSGLYACVTNSPSGSDTTYFSVNVS
          LLQL.CRLR.DVQSIN.L...VQL.ES.RT.ITGEEVEV.DSIPADSGLYACVT.SPSGSDTTYFS.NVS
Retrocopy LLQLHCRLRNDVQSINSL--WVQLVESSRTHITGEEVEVQDSIPADSGLYACVTSSPSGSDTTYFSANVS

Parental  DALPSSEDDDDDDDSSSEEKETDNTKPNRRPVAPYWTSPEKMEKKLHAVPAAKTVKFKCPSSGTPSPTLR
          DALPSSEDDDDDDDSSSEEK.TD.TKPN.RPVAPYWTSPEKME.KLHAVPAAKTVKFKCPSSGTPSPTLR
Retrocopy DALPSSEDDDDDDDSSSEEKGTDTTKPNHRPVAPYWTSPEKMERKLHAVPAAKTVKFKCPSSGTPSPTLR

Parental  WLKNGKEFKPDHRIGGYKVRYATWSIIMDSVVPSDKGNYTCIVENEYGSINHTYQLDVVERSPHRPILQA
          WLKNGKEFKPDH.IGGYKV.YATWSII.DSVVP..KGNYTC..ENEYGSINHTYQLDVVERSPHRPILQA
Retrocopy WLKNGKEFKPDH*IGGYKVHYATWSIIVDSVVPFNKGNYTCTMENEYGSINHTYQLDVVERSPHRPILQA

Parental  GLPANKTVALGSNVEFMCKVYSDPQPHIQWLKHIEVNGSKIGPDNLPYVQILKTAGVNTTDKEMEVLHLR
          GLPANKTVA.GS.VEFMCKVYSDPQPHIQWLKHI..NGSKIGPD.LPYVQILKTAGVNTTDKEMEVLHLR
Retrocopy GLPANKTVAPGSTVEFMCKVYSDPQPHIQWLKHIKMNGSKIGPDSLPYVQILKTAGVNTTDKEMEVLHLR

Parental  NVSFEDAGEYTCLAGNSIGLSHHSAWLTV-LEALEERPAVMTSPLYLEIIIYCTGAFLISCMVGSVIIYK
          NVSFEDAG.YTCLAGNSIGLSHHS.WLTV..EALEER.A.MTSPLYLEIIIYCTGAFLISCM.G.V.IYK
Retrocopy NVSFEDAGGYTCLAGNSIGLSHHSTWLTV<WEALEERQAMMTSPLYLEIIIYCTGAFLISCMLGPVVIYK

Parental  MKSGTKKSDFHSQMAVHKLAKSIPLRRQVTVSADSSASMNSGVLLVRPSRLSSSGTP-MLAGVSEYELPE
          MKSG.KKSDFHSQMAVHKLAKS..L.RQVTVSADSSASMNSGV.LV.PS.LSSSGTP.MLAGVSEY.LPE
Retrocopy MKSGIKKSDFHSQMAVHKLAKSTLLCRQVTVSADSSASMNSGVHLV*PS*LSSSGTP>MLAGVSEYDLPE

Parental  DPRWELPRDRLVLGKPLGEGCFGQVVLAEAIGLDKDKPNRVTKVAVK-MLKSDATEKDLSDLISEMEMMK
          DP.WELPRDRLVL.KPLG.G.FGQVVLAEAIGLDKDKPNR.TKVA.K.MLKS..TEKDLSDLISEMEMMK
Retrocopy DPCWELPRDRLVLRKPLGKG-FGQVVLAEAIGLDKDKPNRMTKVAEK>MLKSNETEKDLSDLISEMEMMK

Parental  MIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYCYNPSHNPEEQLSSKDLVSCAYQ
          MIGKHKNIINLLG.CTQD..LYVIV.YA.KGNL.EYLQARRPPGLE.CY.PSHNPEEQLSSKDLVSCAYQ
Retrocopy MIGKHKNIINLLGVCTQDDSLYVIVDYAPKGNLWEYLQARRPPGLE*CYSPSHNPEEQLSSKDLVSCAYQ

Parental  VARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGR-LPVKWMAPEALFDR
          V..GMEYLASKK.IH.DLAARNVLVTED.VM.IADFGLARDIHHID.Y.K.T....LPVKWMAPEALFDR
Retrocopy VVWGMEYLASKKFIH*DLAARNVLVTEDKVMMIADFGLARDIHHID-YYKKTTNV>LPVKWMAPEALFDR

Parental  IYTHQSDVWSFGVLLWEI
          IY.....V...G.L....
Retrocopy IYIPEGWVVFWGALVGDL

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	0.07 RPM	55.00 RPM
SRP017611_kidney	0.14 RPM	105.51 RPM
SRP017611_liver	0.00 RPM	6.05 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2064 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2064 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2064 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	ENSRNOG00000016050	1 retrocopy	retro_rnor_2064 ,