RetrogeneDB ID: retro_rnor_2831

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:84602031..84602949(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000004848
• 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_2831
CATGCAGGTGTCTATACAGCTGAGGAGGTGGCTCGTATTATGAGAGAAAAGCTGATACGTTTGCAGTCTTTGTACATTGA
TCAGTTTAAACGACTACAGCACCTGCTCAAAGAGAAGAAGCGCCGTTACTTACATAATCGGAAAGTGGAACACGAAGCTT
TAGGTAGTAGTCTCCTGACTGGCCCCCAGGGACTTTGGGCCAAAGAGAGAGAGAATTTAAAGCGACTAAAATGTCTCAGG
CGATACCACCAACGCTATGGAGTAGAAGCCTTACTACACAGGCAGCTGAAGGAACGCAGAATGCTGGCCACAGAGGGGGC
TGCTCAACAGGCTCATACCACTCGTTCCAGTCAGAGGTGCTTAGCCTTTGTGGATGATGTTCACTGCTCCAATCAGTCTC
TTCCAAAGACCGGACACTGTCTTACCCATATCTGTCAGGATACAAATCAGGTTCTCTTCAAATGCTGCCAGGGATCTGAA
GAGGTACCCTGCAACAAGCCAGTTCCTGTTAACCTTTCTGAGGACCCCTGCTGTCCATTGCACTTCCAGTTGCCTCCTCA
GATGTATAAGCCCGAGCAGGTACTGTCTGTGCCAGACGATCTGGAAGCAGGCCCCATTGATCTGTACTTGAGTGCTGTCG
AGCTTCAGCCCACTCAAAGTTTACCACTGGAGTTCATTGATGACTTGGTGTCTTAGGTGATGGCATGCCATGCCCTCCAT
CACCCTTGCTCTTTGATCCCTCCCTAACTCTAGATGATCATTCCGTCACAGAAATTGCCGGAGGCTCAGGAGAGATACAG
GTGGCTGGGGATGGGTGCAGATCCCAGGGACGTCATAATGTAGAGAAAAACCTGTGCATCATTCCCTCAGCGTGGATTGG
CTACTGCAAATGGAAAACCAGAGCCCACTTTTATCAGT

Alignment

ORF - retro_rnor_2831 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.21 %
• Parental protein coverage: 62.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HAGVYTAEEVALIMREKLIRLQSLYIDQFKRLQHLLKEKKRRYLHNRKVEHEALGSSLLTGPEGLLAKER
          HAGVYTAEEVA.IMREKLIRLQSLYIDQFKRLQHLLKEKKRRYLHNRKVEHEALGSSLLTGP.GL.AKER
Retrocopy HAGVYTAEEVARIMREKLIRLQSLYIDQFKRLQHLLKEKKRRYLHNRKVEHEALGSSLLTGPQGLWAKER

Parental  ENLKRLKCLRRYRQRYGVEALLHRQLKERRMLATEGAAQQAHTTRSSQRCLAFVDDVRCSNQSLPMTRHC
          ENLKRLKCLRRY.QRYGVEALLHRQLKERRMLATEGAAQQAHTTRSSQRCLAFVDDV.CSNQSLP.T.HC
Retrocopy ENLKRLKCLRRYHQRYGVEALLHRQLKERRMLATEGAAQQAHTTRSSQRCLAFVDDVHCSNQSLPKTGHC

Parental  LTHICQDTNQVLFKCCQGSEEVPCNKPVPVSLSEDPCCPLHFQLPPQMYKPEQVLSVPDGLEAGPMDLYL
          LTHICQDTNQVLFKCCQGSEEVPCNKPVPV.LSEDPCCPLHFQLPPQMYKPEQVLSVPD.LEAGP.DLYL
Retrocopy LTHICQDTNQVLFKCCQGSEEVPCNKPVPVNLSEDPCCPLHFQLPPQMYKPEQVLSVPDDLEAGPIDLYL

Parental  SAAELQPTESLPLELSDD-LDVVGDGMPCPPSPLLFDPSLTLEDHSVTEIAGGPGQIQVAGDGCRSQGPH
          SA.ELQPT.SLPLE..DD.L.V.GDGMPCPPSPLLFDPSLTL.DHSVTEIAGG.G.IQVAGDGCRSQG.H
Retrocopy SAVELQPTQSLPLEFIDD<LGVLGDGMPCPPSPLLFDPSLTLDDHSVTEIAGGSGEIQVAGDGCRSQGRH

Parental  NVE-KTCAPFPQRGLATANGKPEPTSIS
          NVE.KTCA.FPQRGLATANGKPEPT.IS
Retrocopy NVE>KTCASFPQRGLATANGKPEPTFIS

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_2831 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2831 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2831 has 0 orthologous retrocopies within eutheria group .

---

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,