RetrogeneDB ID: retro_mmus_1099

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:51205262..51206077(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cttn
• Ensembl ID: ENSMUSG00000031078
• Aliases: Cttn, 1110020L01Rik, Ems1
• Description: cortactin [Source:MGI Symbol;Acc:MGI:99695]

Sequence

>retro_mmus_1099
CAGACAGACAGACAGGACAAGTGTGCCCTTGGCTGGGACCATCAGGAGAAGCTGCAGCTGCATTAATCCCAAAAAGACTA
TGCCAAAGGATTCGGCGGGAAGTATGGGGTGCAGAAGGATCGGATGGACAAGAATGCATCCACCTTTGAAGAAGTGGTCC
AGGTGCCGTCTGCCTATCAGAAGACTGTCCCCATTGAGGCCATAACCAGCAAAACCAGTAATATCCGTGCTAACTTGGAA
AACCTGGCAAAGGAGAGAGAGCAGGAGGACAGGCGGAAGGCAGAAGCCGAGAGAGCTCAGAGGATGGCCAATGAAAGACA
GAAGCAGGAGGAGGCGCACAGGAGGCTGGAAGAGCAGGCCAGAGCCAAGAAGCAGACGCCCCCTGCATCCCCCTAGTCCT
CAACCAATTGAAGACAGACCACCCTCCAGCCCCATCTATGAGGATGCAGCTCTGTTCAAGGCCGAGCCGAGCTACCGAGG
TAGCGAACCTGAGCCCGAGTACAGCATCGAGGCCGCAGGTGTTCCTGAGGCTGGCAGCCAGCAAGGCCTGACCTATACAT
CGGAGCCCGTGTACGAGACCACAGAGGCTCCTGGCCACTACCAAGCAGAGGATGACACCTACGATGGGTATGAGAGTGAC
CTGGGCATCACAGCCATCGCCCTGTATGACTACCAGGTTGCGGGCAATGGTGAGCTCTCCCTTTGACCCTGATGACATCA
TCATCAACATAGAAATGATTGAGGATGGCTGGTGGCGTGGGGTGTGCAAGGGCAGATACGGACTCTTCCCAGCTAACTAT
GTGGAGCTGCGGCAG

Alignment

ORF - retro_mmus_1099 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.77 %
• Parental protein coverage: 53.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QTDRQDKCALGWDHQEKLQLHESQKDYAKGFGGKYGVQKDRMDKNASTFEEVVQVPSAYQKTVPIEAVTS
          QTDRQDKCALGWDHQEKLQLH.SQKDYAKGFGGKYGVQKDRMDKNASTFEEVVQVPSAYQKTVPIEA.TS
Retrocopy QTDRQDKCALGWDHQEKLQLH*SQKDYAKGFGGKYGVQKDRMDKNASTFEEVVQVPSAYQKTVPIEAITS

Parental  KTSNIRANFENLAKEREQEDRRKAEAERAQRMAKERQEQEEARRKLEEQARAKKQTPPAS-PSPQPIEDR
          KTSNIRAN.ENLAKEREQEDRRKAEAERAQRMA.ERQ.QEEA.R.LEEQARAKKQTPPAS.PSPQPIEDR
Retrocopy KTSNIRANLENLAKEREQEDRRKAEAERAQRMANERQKQEEAHRRLEEQARAKKQTPPAS>PSPQPIEDR

Parental  PPSSPIYEDAAPFKAEPSYRGSEPEPEYSIEAAGIPEAGSQQGLTYTSEPVYETTEAPGHYQAEDDTYDG
          PPSSPIYEDAA.FKAEPSYRGSEPEPEYSIEAAG.PEAGSQQGLTYTSEPVYETTEAPGHYQAEDDTYDG
Retrocopy PPSSPIYEDAALFKAEPSYRGSEPEPEYSIEAAGVPEAGSQQGLTYTSEPVYETTEAPGHYQAEDDTYDG

Parental  YESDLGITAIALYDYQAAGDDEIS-FDPDDIITNIEMIDDGWWRGVCKGRYGLFPANYVELRQ
          YESDLGITAIALYDYQ.AG..E.S.FDPDDII.NIEMI.DGWWRGVCKGRYGLFPANYVELRQ
Retrocopy YESDLGITAIALYDYQVAGNGELS>FDPDDIIINIEMIEDGWWRGVCKGRYGLFPANYVELRQ

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	0.37 RPM	104.83 RPM
SRP007412_cerebellum	0.65 RPM	91.97 RPM
SRP007412_heart	0.00 RPM	57.22 RPM
SRP007412_kidney	0.56 RPM	127.49 RPM
SRP007412_liver	0.33 RPM	56.80 RPM
SRP007412_testis	0.23 RPM	47.29 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1099 was not detected

EST

No EST(s) were mapped for retro_mmus_1099 retrocopy.

TSS

No TSS is located nearby retro_mmus_1099 retrocopy 5' end.

Lab

retro_mmus_1099 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1099 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000031078	2 retrocopies	retro_mmus_1099 , retro_mmus_2833,