RetrogeneDB ID: retro_rnor_1211

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:8928663..8929143(-)
• Located in intron of: ENSRNOG00000020291

Retrocopy information

• Ensembl ID: ENSRNOG00000020292
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Zwint
• Ensembl ID: ENSRNOG00000048682
• Aliases: Zwint, Sip30, Zwint-1
• Description: ZW10 interactor [Source:UniProtKB/Swiss-Prot;Acc:Q8VIL3]

Sequence

>retro_rnor_1211
GAGGAACCAGATGCTTTGGTCTCTGAAGACACAAGTCAACAAAAGGCAACTGGAACTAAGAAGCAGTCGAAGGAACTGAA
GGCCACATACTCGGATCATGTGGATATCATAAAATGTGCCGTGTCTGAGGCCTTACCCCAGGTTAAAGAGGCTCACAGGA
AGTACACAGAGCTTCAGAAGGTGTTTGAGCAACTCAAGCTAAGAAGTGAGTCCTTGAGGAGAAACTATAATTAGCTCAGA
AACAGTGGGTGCTGCGACAGAGTCTGACAAAGATTTCTGCAGAGGTAAAGAGACGCTGGAAGAGAGCTCTGGAGAAGCTT
GGTGGCTCACATCAGGAGCTTGAGACCTTGAGGCCGCAAGCAGGACAGAAACAGGAGAAACCGCAGAGGAACTAGAGCTA
CTCCAGCTGCTGTGTTCCCTGCAGAATAAGCTGTCATCTCCGAGGACAGAGATGTCAGAGGGCCCGCCCTTCCACCCAAG

Alignment

ORF - retro_rnor_1211 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.07 %
• Parental protein coverage: 63.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QNPDALASEDTSRQKATETKEQWKELKATYMDHVDVIKCALSEALPQVKEAHRKYTELQKAFEQL-EAKK
          ..PDAL.SEDTS.QKAT.TK.Q.KELKATY.DHVD.IKCA.SEALPQVKEAHRKYTELQK.FEQL..AKK
Retrocopy EEPDALVSEDTSQQKATGTKKQSKELKATYSDHVDIIKCAVSEALPQVKEAHRKYTELQKVFEQL<QAKK

Parental  RVLEEKLQLAQKQWVLQQKRLQNLTKISAEVKRRRKRALEKLDGSHQELETLKQQAGQEQEKLQRNQSY-
          .VLEEKL.LAQKQWVL.Q.....LTKISAEVKRR.KRALEKL.GSHQELETL..QAGQ.QEK.QRN.SY.
Retrocopy *VLEEKL*LAQKQWVLRQ----SLTKISAEVKRRWKRALEKLGGSHQELETLRPQAGQKQEKPQRN*SY<

Parental  LQLLCSLQNKL-VISESKADDKDVKGPALPPK
          LQLLCSLQNKL.VISE....D.DV.GPALPPK
Retrocopy LQLLCSLQNKL<VISE----DRDVRGPALPPK

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	2065.87 RPM
SRP017611_kidney	0.07 RPM	110.12 RPM
SRP017611_liver	0.34 RPM	22.12 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1211 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1211 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1211 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002655	1 retrocopy	retro_btau_239,
Echinops telfairi	ENSETEG00000007793	1 retrocopy	retro_etel_261,
Mus musculus	ENSMUSG00000019923	3 retrocopies	retro_mmus_1488, retro_mmus_2611, retro_mmus_997,
Rattus norvegicus	ENSRNOG00000048682	2 retrocopies	retro_rnor_1211 , retro_rnor_1306,
Tarsius syrichta	ENSTSYG00000010283	1 retrocopy	retro_tsyr_1005,
Tursiops truncatus	ENSTTRG00000002204	1 retrocopy	retro_ttru_1193,