RetrogeneDB ID: retro_mmus_2611

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:137928292..137929017(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Zwint
• Ensembl ID: ENSMUSG00000019923
• Aliases: Zwint, 2010007E07Rik, 2600001N01Rik, D10Ertd749e, Zwint-1
• Description: ZW10 interactor [Source:MGI Symbol;Acc:MGI:1289227]

Sequence

>retro_mmus_2611
AGACAAAACGCTGTTGCGACGAAAGAGGTTCTGGCTGAGGCAGCAGCCATTCTAGAACCTGTAGGCTTGCAGGAAGAAGC
AGAGCTGCCTGCCAAGATCATGGAGGAGTTCATGAGGAAGTCGCGGAAGAAAGACAAACTGCTTTGTAGCCAGCTTCAAG
TAGTGAACTTCTTACAGACTTCTCTGCCTCAGGAGGATACTGACCAGAATCCAGATGCTTTGGCTTCTGAAGATGCAAGT
CGGCAAAAGGCAACTGAAACTAAGGAGCAGTAAAAGGACATGAAGGCCACATACATGGATCACGTGGATGTCATAAAATG
GGCCCTGTTGGAGGCCTTACCCCAGGTTAAAGAGGCTCACAGGAATTACAAAGAGCTTCAGAAGGCTTTTGAGCAACTCG
AGGCTAAGAAGCGAGTCCTTGAGGAGAAACTTCAGCTGGCTCAGAAGCAGTGGGCGCTGCAACAGAAGCGTTTGCAGAAT
CTGACAAAGACGTCTGCAGAGGTCAAGAGGCGCCGCGGGAAGAGGGCTCTGGAGAAGCTTGACGGACCCCACCAGGAACT
GGAAACCTTGAAGCAGCAAGCGGGACAGGAACAGGGGAAGCTGCAGAGGAACCAGAGCTACCTCCAGCTGCTGTGTTCCC
TGCAGAATAAGCTGGTCATCTCTGAGGGCAAGGCTGAGGACAAAATGTCAAAGGGCGAGCCCTTACAGCCAAATCCAAAT
CTCCT

Alignment

ORF - retro_mmus_2611 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.18 %
• Parental protein coverage: 95.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KNNAVATKEVLAEAAAILEPVGLQEEAELPAKIMEEFMRNSRKKDKLLCSQLQVVNFLQTFLAQEDTEQS
          ..NAVATKEVLAEAAAILEPVGLQEEAELPAKIMEEFMR.SRKKDKLLCSQLQVVNFLQT.L.QEDT.Q.
Retrocopy RQNAVATKEVLAEAAAILEPVGLQEEAELPAKIMEEFMRKSRKKDKLLCSQLQVVNFLQTSLPQEDTDQN

Parental  PDALASEDASRQKATETKEQWKDMKATYMDHVDVIKCALSEALPQVKEAHRKYTELQKAFEQLEAKKRVL
          PDALASEDASRQKATETKEQ.KDMKATYMDHVDVIK.AL.EALPQVKEAHR.Y.ELQKAFEQLEAKKRVL
Retrocopy PDALASEDASRQKATETKEQ*KDMKATYMDHVDVIKWALLEALPQVKEAHRNYKELQKAFEQLEAKKRVL

Parental  EEKLQLAQKQWVLQQKRLQNLTKISAEVKRRR-KRALEKLDGSHQELETLKQQAGQEQEKLQRNQSYLQL
          EEKLQLAQKQW.LQQKRLQNLTK.SAEVKRRR.KRALEKLDG.HQELETLKQQAGQEQ.KLQRNQSYLQL
Retrocopy EEKLQLAQKQWALQQKRLQNLTKTSAEVKRRRGKRALEKLDGPHQELETLKQQAGQEQGKLQRNQSYLQL

Parental  LCSLQNKLVISEGKAEDK-DVKGRALTAKSKSP
          LCSLQNKLVISEGKAEDK..VKGRALTAKSKSP
Retrocopy LCSLQNKLVISEGKAEDK<NVKGRALTAKSKSP

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
SRP007412_brain	0.30 RPM	713.71 RPM
SRP007412_cerebellum	0.13 RPM	405.77 RPM
SRP007412_heart	0.09 RPM	37.51 RPM
SRP007412_kidney	0.13 RPM	61.54 RPM
SRP007412_liver	0.03 RPM	42.74 RPM
SRP007412_testis	0.00 RPM	46.61 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2611 was not detected

EST

No EST(s) were mapped for retro_mmus_2611 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_111172	710 libraries	310 libraries	51 libraries	1 library	0 libraries

The graphical summary, for retro_mmus_2611 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_2611 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2611 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,