RetrogeneDB ID: retro_rnor_1071

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:86594129..86595257(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000030988
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Kansl2
• Ensembl ID: ENSRNOG00000010904
• Aliases: Kansl2, RGD1303127
• Description: KAT8 regulatory NSL complex subunit 2 [Source:UniProtKB/Swiss-Prot;Acc:Q6AY70]

Sequence

>retro_rnor_1071
CAGGCCCTATTGTGCCAGTTGAGCTCATATACTAAAACAGAGCTGGGCTCGCAGACCCCAGAGAGTAGCCGAAGCGAGGC
GAGCCGGATACTGGATGAAGACAGCTGGAGTGATGGGGACCAGGAACCCATTACTGTGGATCAGACATGGAGAGGTGACC
GTGACAGTGAAGCTGATAGCATAGACAGTGATCAAGAAGATCCCCTAAAACATGCGGGCATCTATACAGCCGAGGAGGTG
GCTCTTATCATGAGAGAAAAGCTGATTCGTTTGCAGTCTTTGTACATTGATCAGTTTAAACGACTACAGCACCTGCTCAA
AGAGAAGAAGCGCCGTTACTTACATAATCGGAAAGTGGAGCACGAAGCTTTAGGTAGTAGTCTCCTGACTGGCCCCGAGG
AACTTTTGGCCAAAGAGAGAGAGAATTTAAAAGCGACTAAAATGTCTCAGGCGATACCGTCAACTCTATGGAGTAAAGCC
TTACTACACAGGCAGCTGAAGGAACGCAGAATGCTGGCCACAGAGGGGGCTGCTCAACGGGCTCAGACCACTCGTTCCAG
TCAGAGGTGCTTAGACTTTGTGGATGATGTTCGCTGCTCCAATCAGTCTCTTCCGATGACCAGACACTGCCTTACCCATA
TCTGTCAGGATACAAATCAGGTTCTCTTCAAATGCTGCCAGGGATCTGCAGAGGTACCCTGCAACAAACCAGTTCCTGTA
AGCCTTTCTGAGGACCCCTGCTGTCCACTGCACTTCCAGTTGCCTCCTCAGATGTATAAGCCCGAGCAGGTACTGTCTGT
GCCAGACGACCTAGAAGCCGACCCCATGGATCTGTACTTGAGTGCTGCCGAGCTTCAGCCCACTGAGAGCTTACCACTGG
GGCTCAGTGACGACTTGGATGTCGTAGGTGATGGCATGCCGTGCCCTCCATCGCCCTTGCTCTTTGATCCCTCCCTAACT
CTAGAAGATCATTCCGTCACTGAAATTGCTGGAGGCCCAGGACAGATACAGGTGGCTGGGGATGGGTGCAGATCCCAGGG
ACCTCATAATGTAGAGAAAACCTGTGCACCATTCCCTCAGCGTGGATTGGCTACTGCAAATTGAAAACCAGAGCCCACTT
CTATCAGT

Alignment

ORF - retro_rnor_1071 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.24 %
• Parental protein coverage: 77.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ETLLCQLSSYAKTELGSQTPESSRSEASRILDEDSWSDGDQEPITVDQTWRGDPDSEADSIDSDQEDPLK
          ..LLCQLSSY.KTELGSQTPESSRSEASRILDEDSWSDGDQEPITVDQTWRGD.DSEADSIDSDQEDPLK
Retrocopy QALLCQLSSYTKTELGSQTPESSRSEASRILDEDSWSDGDQEPITVDQTWRGDRDSEADSIDSDQEDPLK

Parental  HAGVYTAEEVALIMREKLIRLQSLYIDQFKRLQHLLKEKKRRYLHNRKVEHEALGSSLLTGPEGLLAKER
          HAG.YTAEEVALIMREKLIRLQSLYIDQFKRLQHLLKEKKRRYLHNRKVEHEALGSSLLTGPE.LLAKER
Retrocopy HAGIYTAEEVALIMREKLIRLQSLYIDQFKRLQHLLKEKKRRYLHNRKVEHEALGSSLLTGPEELLAKER

Parental  ENLK-RLKCLRRYRQRYGVE-ALLHRQLKERRMLATEGAAQQAHTTRSSQRCLAFVDDVRCSNQSLPMTR
          ENLK.RLKCLRRYRQ.YGV..ALLHRQLKERRMLATEGAAQ.A.TTRSSQRCL.FVDDVRCSNQSLPMTR
Retrocopy ENLK>RLKCLRRYRQLYGVK<ALLHRQLKERRMLATEGAAQRAQTTRSSQRCLDFVDDVRCSNQSLPMTR

Parental  HCLTHICQDTNQVLFKCCQGSEEVPCNKPVPVSLSEDPCCPLHFQLPPQMYKPEQVLSVPDGLEAGPMDL
          HCLTHICQDTNQVLFKCCQGS.EVPCNKPVPVSLSEDPCCPLHFQLPPQMYKPEQVLSVPD.LEA.PMDL
Retrocopy HCLTHICQDTNQVLFKCCQGSAEVPCNKPVPVSLSEDPCCPLHFQLPPQMYKPEQVLSVPDDLEADPMDL

Parental  YLSAAELQPTESLPLELSDDLDVVGDGMPCPPSPLLFDPSLTLEDHSVTEIAGGPGQIQVAGDGCRSQGP
          YLSAAELQPTESLPL.LSDDLDVVGDGMPCPPSPLLFDPSLTLEDHSVTEIAGGPGQIQVAGDGCRSQGP
Retrocopy YLSAAELQPTESLPLGLSDDLDVVGDGMPCPPSPLLFDPSLTLEDHSVTEIAGGPGQIQVAGDGCRSQGP

Parental  HNVEKTCAPFPQRGLATANGKPEPTSIS
          HNVEKTCAPFPQRGLATAN.KPEPTSIS
Retrocopy HNVEKTCAPFPQRGLATAN*KPEPTSIS

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	48.03 RPM
SRP017611_kidney	0.00 RPM	35.59 RPM
SRP017611_liver	0.00 RPM	24.34 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1071 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1071 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1071 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005760	1 retrocopy	retro_cpor_1491,
Dipodomys ordii	ENSDORG00000001180	1 retrocopy	retro_dord_474,
Mus musculus	ENSMUSG00000022992	2 retrocopies	retro_mmus_2944, retro_mmus_3134,
Rattus norvegicus	ENSRNOG00000010904	3 retrocopies	retro_rnor_1071 , retro_rnor_2831, retro_rnor_792,
Tupaia belangeri	ENSTBEG00000016536	1 retrocopy	retro_tbel_1374,