RetrogeneDB ID: retro_mmus_2938

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:61938236..61938911(+)
• Located in intron of: ENSMUSG00000097225

Retrocopy information

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

Parental gene information

• Parental gene symbol: Snrpb
• Ensembl ID: ENSMUSG00000027404
• Aliases: Snrpb, AL024368, AU018828, SM-B, SM11, SMB, SNRNP-B
• Description: small nuclear ribonucleoprotein B [Source:MGI Symbol;Acc:MGI:98342]

Sequence

>retro_mmus_2938
ATGACTGTGAACAATAGCAACAAGATGGTGCAGCACATTAACTACAGGATGAGAGGCATCCTGCAAAATGGCTAGATCTT
TACTGGACCTTCAAAGCATTTGACAAGCATATGAATTTATCTTCTGTGTCTGTGATGAGTTCAGGAAGATTAAGCTAAAG
AACTCCAAACAAGCAGAAATAGAAGAGAAGTGAGTCATTGTTCTGGTGTTGCTTTATGGGGGAGAACCTGGTCTACACGA
CAGTAGAAGGACCTCCTCCTCCTAAAGATACTGGCATTGCCCGAGTGCCAATTGTTGAAGCTGCTGGATGGCCAGGTATT
CTCAAGGCTGCTAGAAGAGGAATCCCATCTGGTGTTCCCATGCCCCAAGTTCCTGTAGGTTTTTCTGGGCTAGTATGAGA
TATTGGAGGGTCATCCCAGAAGGTGATGACCCCACAAGGAAGAGTTACTGTTGCAGCTGCAGCCAGAGCCAGTAATGCAG
GAGTCTCAACTCAGTACACACCTGGTAATGGGTGTCCTCCTCCACCTATGGGTAAAGGGGTCTCCTCCAGGTATAATGGG
CCCATGTCCTGGCAAGAGGTCTCCCATTCGTGCCCCAATGGGATCCCTCCTGGCTGAGGAACTCCAATGGGTATGACCCC
TTCCTGGGATGTAAACTCCTTCTCCAGGAATGCAG

Alignment

ORF - retro_mmus_2938 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.94 %
• Parental protein coverage: 98.7 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MTVGKSSKMLQHIDYRMRCILQDGRIFIG-TFKAFDKHMNL-ILCDCDEFRKIKPKNSKQAEREEKRVLG
          MTV..S.KM.QHI.YRMR.ILQ.G.IF.G.TFKAFDKHMNL.I.C.CDEFRKIK.KNSKQAE.EEK.V..
Retrocopy MTVNNSNKMVQHINYRMRGILQNG*IFTG<TFKAFDKHMNL<IFCVCDEFRKIKLKNSKQAEIEEK*VIV

Parental  LVLL-RGENLVSMTVEG-PPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGG
          LVLL..GENLV..TVEG.PPPKDTGIARVP...AAG.PGI..AA.RGIP.GVPMPQ.P.G..G.V...GG
Retrocopy LVLL>MGENLVYTTVEGPPPPKDTGIARVPIVEAAGWPGILKAARRGIPSGVPMPQVPVGFSGLV*DIGG

Parental  PSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMG-RGAPPPGMMGPPPGMRPPMGPPM-G
          .SQ.VMTPQGR.TVAAAA.A..A...G..TQY.PG.G.PPPPMG..G.P.PG.MGP.PG.R.P...PM.G
Retrocopy SSQKVMTPQGRVTVAAAARASNA---GVSTQYTPGNGCPPPPMG>KGSP-PGIMGPCPGKRSPIRAPM<G

Parental  LPPGRGTPMGMPP-PGMRPPPPGMR
          .PPG.GTPMGM.P.PGM..P.PGM.
Retrocopy IPPG*GTPMGMTP>PGM*TPSPGMQ

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	0.82 RPM	36.68 RPM
SRP007412_cerebellum	2.30 RPM	37.69 RPM
SRP007412_heart	0.00 RPM	45.67 RPM
SRP007412_kidney	0.02 RPM	41.52 RPM
SRP007412_liver	0.00 RPM	24.74 RPM
SRP007412_testis	0.00 RPM	32.52 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2938 was not detected

EST

No EST(s) were mapped for retro_mmus_2938 retrocopy.

TSS

No TSS is located nearby retro_mmus_2938 retrocopy 5' end.

Lab

retro_mmus_2938 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2938 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006693	3 retrocopies	retro_cfam_1268, retro_cfam_1773, retro_cfam_461,
Callithrix jacchus	ENSCJAG00000020971	2 retrocopies	retro_cjac_172, retro_cjac_1739,
Mus musculus	ENSMUSG00000000948	3 retrocopies	retro_mmus_1285, retro_mmus_1733, retro_mmus_665,
Mus musculus	ENSMUSG00000027404	3 retrocopies	retro_mmus_2938 , retro_mmus_3450, retro_mmus_554,
Otolemur garnettii	ENSOGAG00000016149	4 retrocopies	retro_ogar_2197, retro_ogar_2841, retro_ogar_2918, retro_ogar_3236,
Rattus norvegicus	ENSRNOG00000006961	2 retrocopies	retro_rnor_2825, retro_rnor_474,