RetrogeneDB ID: retro_mmus_2813

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:37686346..37687195(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ybx1
• Ensembl ID: ENSMUSG00000028639
• Aliases: Ybx1, 1700102N10Rik, C79409, EF1A, MSY1, Nsep1, YB-1, dbpB, mYB-1a
• Description: Y box protein 1 [Source:MGI Symbol;Acc:MGI:99146]

Sequence

>retro_mmus_2813
ATGAGCAGCGAGGCAGAGACCCAGCAGCTGCCCGTCGCCCCCGCAGCCACCCTCAGTGCTGCCACCACCAAGCCCAGTTC
CACAGGCAGCGGCGGCGCCGGTAGTGGTGGCCCGGGCGGCCTCACATTGGCGGCGCCCACCAGCAGGGACAAGAAGGTCA
TCACAACGAAGGTTTTGGGAACAGTCAGATGGATCAATGTAAGGAACGGATACAGTTTCATCAACAGGAATGACACCAAG
GAAGACGTATTTGTACACCAGACTGCCATAAGGAAGAATAACCCCAGGAAGTACCTTCGCAGTGTAGGCGATGGAGAGAC
TGTGGAGTTTGATGTTGTTGAAGGAGAAAAGGGTGCGGAGGCAGCAAAAGTTACAGGCCCTGGTGGAGTTCCAGTTCAAG
GCAGTAAATACGCAGCAGACCGTAACCATTATAGACGCTATCCACGTCGTAGGGGTCCTCCACGCAATTACCAGCAAAAT
TACCAGAATAGTGAGAGTGGGGAAAAGAACGAGGGATCAGAAAGCTCTCCTGAAGGCCAGGCCCAACAACGCTGGCCCTG
TCGCAGGCGAAGGCGAAGGTTCCCACCTTACTACATGAGGAGGCCCAATGCGCGTCGACCACAGAATTCCAACCCCCCTG
TGCAAGGAGAAGTGATGGAGGGTGCTGACAGCCAGGGTGCAGGAGAGCAAGGTAGACCAGTGAGACAGAATATGTATCGG
GGTTACAGACCACGATTCCGAAGGGGCCCTCCTCTCCAAAGACAGCCTAGAGAGGATGGCAATGAAGAGGACAAAGAAAG
TCAAGATGATACCCAAGGTCGGTATCGCAGCAACTTCAATTACCGACGC

Alignment

ORF - retro_mmus_2813 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.68 %
• Parental protein coverage: 87.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSEAETQQPPAAPAAALSAADTKPGSTGSG-AGSGGPGGLTSAAPAGGDKKVIATKVLGTVKWFNVRNG
          MSSEAETQQ.P.APAA.LSAA.TKP.STGSG.AGSGGPGGLT.AAP...DKKVI.TKVLGTV.W.NVRNG
Retrocopy MSSEAETQQLPVAPAATLSAATTKPSSTGSGGAGSGGPGGLTLAAPTSRDKKVITTKVLGTVRWINVRNG

Parental  YGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPGGVPVQGSKYAAD
          Y.FINRNDTKEDVFVHQTAI.KNNPRKYLRSVGDGETVEFDVVEGEKGAEAA.VTGPGGVPVQGSKYAAD
Retrocopy YSFINRNDTKEDVFVHQTAIRKNNPRKYLRSVGDGETVEFDVVEGEKGAEAAKVTGPGGVPVQGSKYAAD

Parental  RNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRRP--YRRRRFPPYYMRRPYARRPQYS
          RNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSES.PEGQAQQR.P...RRRRFPPYYMRRP.ARRPQ.S
Retrocopy RNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSESSPEGQAQQRWPCRRRRRRFPPYYMRRPNARRPQNS

Parental  NPPVQGEVMEGADNQGAGEQGRPVRQNMYRGYRPRFRRGPPRQRQPREDGNEEDKENQGDETQGQQPPQR
          NPPVQGEVMEGAD.QGAGEQGRPVRQNMYRGYRPRFRRGPP.QRQPREDGNEEDKE.Q.D.TQG......
Retrocopy NPPVQGEVMEGADSQGAGEQGRPVRQNMYRGYRPRFRRGPPLQRQPREDGNEEDKESQ-DDTQGRYRSNF

Parental  RYRR
          .YRR
Retrocopy NYRR

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	0.02 RPM	68.08 RPM
SRP007412_cerebellum	0.04 RPM	66.22 RPM
SRP007412_heart	1.00 RPM	456.18 RPM
SRP007412_kidney	0.60 RPM	372.40 RPM
SRP007412_liver	0.16 RPM	136.16 RPM
SRP007412_testis	0.82 RPM	864.37 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2813 was not detected

EST

No EST(s) were mapped for retro_mmus_2813 retrocopy.

TSS

No TSS is located nearby retro_mmus_2813 retrocopy 5' end.

Lab

retro_mmus_2813 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2813 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000028639	3 retrocopies	retro_mmus_1623, retro_mmus_2813 , retro_mmus_746,
Rattus norvegicus	ENSRNOG00000023786	1 retrocopy	retro_rnor_13,