RetrogeneDB ID: retro_rnor_1305

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:45273787..45275165(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dctn4
• Ensembl ID: ENSRNOG00000019298
• Aliases: None
• Description: Dynactin subunit 4 [Source:UniProtKB/Swiss-Prot;Acc:Q9QUR2]

Sequence

>retro_rnor_1305
ATGGCATCCTTGCTACAGTCGGAGTGGGTTCTCCATCTCGTCCAAGGAGAAAAGAAGTTCGGGGCCCACTCTCACAGCTC
TACTTCTGCCGATACTGCAGTGAGCTTCGATCGCTAGAATGTATGCCACACAAGGTGGACTCGAATTATTGTCCCAGCTG
CTTAGAAAACATGCCATCAGCTGAAGCCAAATTAAAAAAGAAAAATGTGCCAACTGCTTTGACTGTCCTGGATGCATGCA
CACCCTTTCCACCTGAGCTACAAGCATCTCCACACAGCTTCCAGACGACCCAGCCAAAACCACTATGAAGAAAGCCTATT
ATTTGGCCTGTGGATTTTGTCGATGAACATCTAGAGATGTGGGCATGGCAGACAAATCTGTAGCTAGTGGTGGTTGGCAA
GAACCAGAAAATCCTCACGCACAACGGATGAACAAGTTGATTGAATATTACCAGCAGCTTGCCCAGAAGGAAAAGGTTGA
ACGAGATCGCAAGAAACTGGCACAGCGAAGAAATTATATGCCTTTGGCTTTTTCAGGCAAGTACAGCCTTGGGACCAGGC
TTCAGTGACCATGAGCTGGTACATCCATTAGTACACTTGCCGGACTTTCCCTTAGAGAAGGAGAAGACCAGAAGGAGGTA
AAGATTGAGCCAGCTCAGGCTGTCGCTGAAGTGGAGCCTCTGCCTGAAGACTATTACACACGACCAGTGAACCTGACAGA
GATGACCACCCTTCAGCGGCGCCTCTTACAACCTGACCTGCAGCCCGTCTTGGCCTCACAGCTTTATCCTCGACACAAGC
ACCTTCTGATCAAATGGTCCCTGTGCTGTCGGAAATGTGAACACAATTTGAGCAAGCCAGAATTTAATCCAACATCCATC
AAATTCGAAATCCAGTTGGTTGCTGTCAATTATATTCCAGAAGTGAGAAGCATGTCGATCCCCAATCTTTGCTACATGAA
GGAGAGCCAGGTCCTCTTGACTCTTACAAATCCAGTGGAGAACCTCACCCATGTACCTCTGCTGGAGTGCGAGGAAGGGG
ACCCTGATAACATCAACAGCACTGCTAAGGTGGTGGTGTCTCCCAAAGAGCTCATCTTAGCCAGCAAGGATGCAGCAGCA
GAGTACGATGAGCTGGCAGAGCCCCAGGACTTCCAGGATGACCCTGACATTGGAGCTTTCAGAAAAGCCAACAAGGTAGG
CATCTTCATCAAAGTCACCCCACAGCATGAGGAAGGGGAAGTGACCATGTGCTTCAAGATGAAACATGATTTTAAAAACC
TGGCTGCCCCCATCCGCCCTATGGGAGAAAGCGACCAGGGCACAGAAGTCATCTGGCTCACTCAGCATGTGGAACTGAGC
TTTGGCCCTCTTCTTCCT

Alignment

ORF - retro_rnor_1305 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASLLQSERVLYLVQGEKK-VRAPLSQLYFCRYCSELRSLECVSHEVDSHYCPSCLENMPSAEAKLKKN-
          MASLLQSE.VL.LVQGEKK.VR.PLSQLYFCRYCSELRSLEC..H.VDS.YCPSCLENMPSAEAKLKK..
Retrocopy MASLLQSEWVLHLVQGEKK<VRGPLSQLYFCRYCSELRSLECMPHKVDSNYCPSCLENMPSAEAKLKKK<

Parental  RCANCFDCPGCMHTLSTRATSISTQLPDDPAKTTMKKAYYLACGFCRWTSRDVGMADKSVASGGWQEPEN
          .CANCFDCPGCMHTLST.ATSISTQLPDDPAKTTMKKAYYLACGFCR.TSRDVGMADKSVASGGWQEPEN
Retrocopy KCANCFDCPGCMHTLST*ATSISTQLPDDPAKTTMKKAYYLACGFCR*TSRDVGMADKSVASGGWQEPEN

Parental  PHAQRMNKLIEYYQQLAQKEKVERDRKKLARRRNYMPLAFSDKYSLGTRLQRPRAGASISTLAGLSLREG
          PHAQRMNKLIEYYQQLAQKEKVERDRKKLA.RRNYMPLAFS.KYSLGTRLQ.P.AG.SISTLAGLSLREG
Retrocopy PHAQRMNKLIEYYQQLAQKEKVERDRKKLAQRRNYMPLAFSGKYSLGTRLQ*P*AGTSISTLAGLSLREG

Parental  EDQKEVKIEPAQAVAEVEPLPEDYYTRPVNLTEVTTLQQRLLQPDLQPVSASQLYPRHKHLLIKRSLRCR
          EDQKEVKIEPAQAVAEVEPLPEDYYTRPVNLTE.TTLQ.RLLQPDLQPV.ASQLYPRHKHLLIK.SL.CR
Retrocopy EDQKEVKIEPAQAVAEVEPLPEDYYTRPVNLTEMTTLQRRLLQPDLQPVLASQLYPRHKHLLIKWSLCCR

Parental  KCEHNLSKPEFNPTSIKFKIQLVAVNYIPEVRIMSIPNLRYMKESQVLLTLTNPVENLTHVTLLECEEGD
          KCEHNLSKPEFNPTSIKF.IQLVAVNYIPEVR.MSIPNL.YMKESQVLLTLTNPVENLTHV.LLECEEGD
Retrocopy KCEHNLSKPEFNPTSIKFEIQLVAVNYIPEVRSMSIPNLCYMKESQVLLTLTNPVENLTHVPLLECEEGD

Parental  PDNINSTAKVVVPPKELILAGKDAAAEYDELAEPQDFQDDPDIVAFRKANKVGIFIKVTPQREEGDVTVC
          PDNINSTAKVVV.PKELILA.KDAAAEYDELAEPQDFQDDPDI.AFRKANKVGIFIKVTPQ.EEG.VT.C
Retrocopy PDNINSTAKVVVSPKELILASKDAAAEYDELAEPQDFQDDPDIGAFRKANKVGIFIKVTPQHEEGEVTMC

Parental  FKMKHDFKNLAAPIRPMEESDQGTEVIWLTQHVELSFGPLLP
          FKMKHDFKNLAAPIRPM.ESDQGTEVIWLTQHVELSFGPLLP
Retrocopy FKMKHDFKNLAAPIRPMGESDQGTEVIWLTQHVELSFGPLLP

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	0.14 RPM	63.48 RPM
SRP017611_kidney	0.35 RPM	32.10 RPM
SRP017611_liver	2.56 RPM	17.41 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1305 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1305 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1305 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000014234	1 retrocopy	retro_pvam_334,
Rattus norvegicus	ENSRNOG00000019298	1 retrocopy	retro_rnor_1305 ,
Ictidomys tridecemlineatus	ENSSTOG00000013446	1 retrocopy	retro_itri_830,