RetrogeneDB ID: retro_rnor_509

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:187486790..187488556(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Taf5l
• Ensembl ID: ENSRNOG00000018027
• Aliases: None
• Description: TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L [Source:RefSeq peptide;Acc:NP_001100912]

Sequence

>retro_rnor_509
ATGAAACGAGTGCGCAGGGAGCACGTTCAGGTGGCAGTGTCCTGCTACCTCAAACGCCTGCAGTATGTGGACTCAGAAGG
CCCTTTGAAGCAAGGCCTGAGACTCTCACAGACCCCTGAGGAGATGGCGGCCAACCTCACAGTCCAATCAGAATCTGGTT
GTGCCAATGCGGTGTCTGCAGCCCCTTGCCAGGCAGAACCCCAGTAATATGAAGTACAGTTTGGACGACTGAGGAACTTT
CTCACTGATTCTGACTCCCAGTACAGCCATGAAGTTATGCCTCTCCTCTACCCTCTCTTTGTCTACCTCCACCTCAACCT
GGTCTAGAGTGGCCCCAAGAGCACCGTGGAAAGCTTCTATAGCCGCTTCCATGGAATGTTCCTGCAGATTGCAAGTCAGA
AGGACATCATCGAGCAACTGCAGACCACGCAGACCATCCAGGATATTCTGTCAAACTTCCGGCTTCGTGCATTCCTGGAC
AACAAGTATGTGGTCCGTCTCCAGGAAGATAGTTACAACTACCTTATCCGCTACCTCCAAAGTGACAACAACACTGCTCT
GTGCAAGGTGCTCGCCGTGCACATTCACTTGGACGTGCAGCCTGCTAAGAGGACAGACTACCAGCTGTATGCCAGTGGTG
GCTCCTCCCGCAGTGAAAGCAGCAGCCTGGAGCCACCAGATTTGCCCAACCCTATCCTGCAGAATGAGGCTGCCCTGGAG
GTCTTGCAGGAGAGTATCAAGCGGGTCAAGGATGGACCTCCCTCCCTCACCACCATCTGCTTCTACGCCTTCTATAACAC
AGAGCAGCTGCTGAATACCGCAGAGATCTCCTCTGACAGCAAACTGCTGGCTCCTGGGTTTGACAACTCCTGGATAAAGC
TCTGGAGCTTGCGGTCCAAAAAACTGAAGTCAGAGCCCCACCGTGTGGACACATCCCGTGTCCGGCTGGCTTGTGACACT
CTGGAGGAAGAGGAGAGCGAAGACGATGACGTAGGCACGGAAATGAAGATTCTGCGGGGACACTGTGGCCCAGTGTATAG
CACACGGTTCCTCGCGGACAGCTCAGGGCTGCTCTCTTGTTCTGAAGATATGTCCATCAGGTACTGGGACCTGGAGAGCT
TCACCAACACTGTGCTGTATCAGGGACATGCCTACCCTGTGTGGGACGTGGACATCAGCCCCTACATCCTGTACTTTGCC
AGTGGGTCCCATGACCGTACCGCCAGGCTGTGGTCTTTTGATCGGACGTACCCGCTGAGGATATATGCGGGGCACCTGGC
AGATGTGGACTGTGTCAAATTCCACCCCAACTCAAACTACTTAGCTACCGGCTCCACTGACAAAACTGTTCGTCTATGGA
GTGCCCAGCAGGGGAACTCAGTGCGGCTTTTTACAGGTCACCGAGGCCCCGTGCTCTCCCTCTCCTTTTCTCCCAATGGT
AAGTACTTGGCATCTGCTGGTGAGGACCAGTGGTTAAAGTTGTGGGACTTGGCCTCTGGGACACTTTTAAAGAACTGAGA
GGCCACACGGACAGCATCACCAGTCTGGCCTTTAGCCCGGACAGCGGTCTGATTGCTTCTGCCTCCATGGAGAACTCTGT
ATGCGTCTGGGACATCAGAAGCGCGTGCTGCAACACACCAACTGACGGCTCTTCTGGGGAGCTTGTGGGCGTGTACACTG
GGCAGATGAGCAACGTCCTGAGTGTACAGTTCATGGCCTGCAACCTCCTCCTAGTGACTGGAATCACACAAGAGAATCAA
GAACAT

Alignment

ORF - retro_rnor_509 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.78 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKRVRTEQVQVAVSCYLKRRQYVDSEGPLKQGLRLSQTPEEMAANLTVQSESGCANAVSAAPCQAEPQQY
          MKRVR.E.VQVAVSCYLKR.QYVDSEGPLKQGLRLSQTPEEMAANLTVQSESGCANAVSAAPCQAEPQ.Y
Retrocopy MKRVRREHVQVAVSCYLKRLQYVDSEGPLKQGLRLSQTPEEMAANLTVQSESGCANAVSAAPCQAEPQ*Y

Parental  EVQFGRLRNFLTDSDSQYSHEVMPLLYPLFVYLHLNLVQSGPKSTVESFYSRFHGMFLQNASQKDIIEQL
          EVQFGRLRNFLTDSDSQYSHEVMPLLYPLFVYLHLNLV.SGPKSTVESFYSRFHGMFLQ.ASQKDIIEQL
Retrocopy EVQFGRLRNFLTDSDSQYSHEVMPLLYPLFVYLHLNLV*SGPKSTVESFYSRFHGMFLQIASQKDIIEQL

Parental  QTTQTIQDILSNFQLRAFLDNKYVVRLQEDSYNYLIRYLQSDNNTALCKVLAVHIHLDVQPAKRTDYQLY
          QTTQTIQDILSNF.LRAFLDNKYVVRLQEDSYNYLIRYLQSDNNTALCKVLAVHIHLDVQPAKRTDYQLY
Retrocopy QTTQTIQDILSNFRLRAFLDNKYVVRLQEDSYNYLIRYLQSDNNTALCKVLAVHIHLDVQPAKRTDYQLY

Parental  ASGGSSRSESSSLEPPDVPNPILQNEAALEVLQESIKRVKDGPPSLTTICFYAFYNTEQLLNTAEISSDS
          ASGGSSRSESSSLEPPD.PNPILQNEAALEVLQESIKRVKDGPPSLTTICFYAFYNTEQLLNTAEISSDS
Retrocopy ASGGSSRSESSSLEPPDLPNPILQNEAALEVLQESIKRVKDGPPSLTTICFYAFYNTEQLLNTAEISSDS

Parental  KLLAAGFDNSCIKLWSLRSKKLKSEPHCVDTSRVRLACDTLEEEESEDDDVGTEMKILRGHCGPVYSTRF
          KLLA.GFDNS.IKLWSLRSKKLKSEPH.VDTSRVRLACDTLEEEESEDDDVGTEMKILRGHCGPVYSTRF
Retrocopy KLLAPGFDNSWIKLWSLRSKKLKSEPHRVDTSRVRLACDTLEEEESEDDDVGTEMKILRGHCGPVYSTRF

Parental  LADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDVDISPYSLYFASGSHDRTARLWSFDRTYPLR
          LADSSGLLSCSEDMSIRYWDL.SFTNTVLYQGHAYPVWDVDISPY.LYFASGSHDRTARLWSFDRTYPLR
Retrocopy LADSSGLLSCSEDMSIRYWDLESFTNTVLYQGHAYPVWDVDISPYILYFASGSHDRTARLWSFDRTYPLR

Parental  IYAGHLADVDCVKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLSFSPNGKYLASAGEDQ
          IYAGHLADVDCVKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLSFSPNGKYLASAGEDQ
Retrocopy IYAGHLADVDCVKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLSFSPNGKYLASAGEDQ

Parental  RLKLWDLASGTL-FKELRGHTDSITSLAFSPDSGLIASASMDNSVRVWDIRSTCCNTPADGSSGELVGVY
          .LKLWDLASGTL.FKELRGHTDSITSLAFSPDSGLIASASM.NSV.VWDIRS.CCNTP.DGSSGELVGVY
Retrocopy WLKLWDLASGTL<FKELRGHTDSITSLAFSPDSGLIASASMENSVCVWDIRSACCNTPTDGSSGELVGVY

Parental  TGQMSNVLSVQFMACNLLLVTGITQENQEH
          TGQMSNVLSVQFMACNLLLVTGITQENQEH
Retrocopy TGQMSNVLSVQFMACNLLLVTGITQENQEH

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	4.96 RPM
SRP017611_kidney	0.00 RPM	3.42 RPM
SRP017611_liver	0.00 RPM	3.77 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_509 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_509 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_509 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034225	1 retrocopy	retro_btau_1300,
Callithrix jacchus	ENSCJAG00000010986	1 retrocopy	retro_cjac_4042,
Homo sapiens	ENSG00000135801	1 retrocopy	retro_hsap_1750,
Gorilla gorilla	ENSGGOG00000028544	1 retrocopy	retro_ggor_2253,
Pan troglodytes	ENSPTRG00000002091	1 retrocopy	retro_ptro_1216,
Rattus norvegicus	ENSRNOG00000012929	1 retrocopy	retro_rnor_2136,
Rattus norvegicus	ENSRNOG00000018027	1 retrocopy	retro_rnor_509 ,