RetrogeneDB ID: retro_mmus_1119

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:74019323..74020089(-)
• Located in intron of: ENSMUSG00000021573

Retrocopy information

• Ensembl ID: ENSMUSG00000080966
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ilk
• Ensembl ID: ENSMUSG00000030890
• Aliases: Ilk, AA511515, ESTM24
• Description: integrin linked kinase [Source:MGI Symbol;Acc:MGI:1195267]

Sequence

>retro_mmus_1119
CGCTTGTGGCTGGACAACACAGAGAATGACCTCAATCAGGGGGGTGATCATGGCTTCTCCCCCTTGCACTGGGCCTGCCG
AGAAGGCAGCTCTGCGGTGGTTGAAATGCTGATCATGCAGGGAGCTCAGATCAATGTGATAATCGTGGGGATGATACCCC
CCTCACCTGGCAGCTAGTCATGGACACCGTGACATTGTACAAAAGCTGTTGCAATACAAGACTGTCATCAATACAGTGAA
TGAGCACGGCAATGTGCCACTTCACTATGCATGTTTCTGGGGCCAAGACCAGGTGGCAGAGGACCTGGTGGCTAACGGGG
CTCTTGGGAGCATCTGTAACAAGTATAGAGAGATGCCTGTGGACAAAGCCAAGGCACCCCTTAGAGAGCTTCTCCCAGAA
CAGGCAGAGAAGATGGGCCAGAATCTCAACCATATTCCATACAAGGACACGTTCTGGAAGGGGACCACTTGCACAAGGCC
CTGAAATGGGACCCTGAACAAACACTCCGGTATTGACTTCAAACAGCTCAACTTTCTGGCAAAGCTCAACAAGAATCATT
CTGGAAAGCTATGAAAAGGCCGCTGGCAGGGCAATGATATTGTTGTGAAGGTGCTGAAGGTTCGAGACTGGAGTACAAGG
AAAAGCAGGGACTTCAATGAGGAATGTCCCCGGCTCAGGATTTTCTCACATCCCAGTGCTAGATACTTGCCAGGCTCCCC
CGGCCCCCCACCCAACCCTCATCACACACTGGATGCCATATGGATC

Alignment

ORF - retro_mmus_1119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.05 %
• Parental protein coverage: 56.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLWLDNTENDLNQGDDHGFSPLHWACREGRSAVVEMLIMRGARINVM-NRGDDTPL-HLAASHGHRDIVQ
          RLWLDNTENDLNQG.DHGFSPLHWACREG.SAVVEMLIM.GA.INV..NRGDDTPL.HLAASHGHRDIVQ
Retrocopy RLWLDNTENDLNQGGDHGFSPLHWACREGSSAVVEMLIMQGAQINVI<NRGDDTPL<HLAASHGHRDIVQ

Parental  KLLQYKADINAVNEHGNVPLHYACFWGQDQVAEDLVANGALVSICNKYGEMPVDKAKAPLRELLRERAEK
          KLLQYK..IN.VNEHGNVPLHYACFWGQDQVAEDLVANGAL.SICNKY.EMPVDKAKAPLRELL.E.AEK
Retrocopy KLLQYKTVINTVNEHGNVPLHYACFWGQDQVAEDLVANGALGSICNKYREMPVDKAKAPLRELLPEQAEK

Parental  MGQNLNRIPYKDTFWKGTTRTRPRNGTLNKHSGIDFKQLNFLAKLNENHSGELWKGRWQGNDIVVKVLKV
          MGQNLN.IPYKDTFWKGTT.TRP.NGTLNKHSGIDFKQLNFLAKLN.NHSG.L.KGRWQGNDIVVKVLKV
Retrocopy MGQNLNHIPYKDTFWKGTTCTRP*NGTLNKHSGIDFKQLNFLAKLNKNHSGKL*KGRWQGNDIVVKVLKV

Parental  RDWSTRKSRDFNEECPRLRIFSHPNVLPVLGACQAPPAPHPTLITHWM
          RDWSTRKSRDFNEECPRLRIFSHP......G....PP.PH.TL...W.
Retrocopy RDWSTRKSRDFNEECPRLRIFSHPSARYLPGSPGPPPNPHHTLDAIWI

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	0.07 RPM	0.12 RPM
SRP007412_cerebellum	0.13 RPM	0.13 RPM
SRP007412_heart	0.09 RPM	0.50 RPM
SRP007412_kidney	0.12 RPM	0.13 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.09 RPM	0.05 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1119 was not detected

EST

No EST(s) were mapped for retro_mmus_1119 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_30998	62 libraries	92 libraries	417 libraries	311 libraries	190 libraries

The graphical summary, for retro_mmus_1119 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_1119 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1119 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016283	1 retrocopy	retro_amel_1547,
Mustela putorius furo	ENSMPUG00000005495	1 retrocopy	retro_mputfur_1297,
Mus musculus	ENSMUSG00000028284	1 retrocopy	retro_mmus_579,
Mus musculus	ENSMUSG00000030890	1 retrocopy	retro_mmus_1119 ,