RetrogeneDB ID: retro_mmus_554

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:40549132..40549559(+)
• Located in intron of: None

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_554
AACCTGGTATCCATGACAGTAGAAGGACCTCTTCCCAAAGATACTGGCATTGCCTGAGTGGCACTTGCTGGAGCTGCTGT
CGGGCCAGGCATCAGCAGGGCTGCTGGCAGAGGAATCCCGGCTGGTGTTCCCATGCCCCAAGCTCCTGCAGGACTTGCTG
GGCCAGTCGAGGTGTTGGAGGGCCATATCCCAACAAATGATGACCCCACAAGGAAGAGGCACTGTTGCAGCTGCTGTAGC
TGCAGCCACAGCCAGTATTGCAGGAGCCCCAACTCAGTACCCACCTGGCCATGGGGCCCCTCCTTCAGGTATGGTGGGCC
CACCTCTTGGCATGTGGCCTCCCATAGGTCCCCCAATGGAGCTCCCTCCTGGCCGAGGAACTCTAATGGCCATGCCCCCT
CCTGGGATGTGGCCTCCTCCTCCAGGC

Alignment

ORF - retro_mmus_554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 65.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPV-RGVGGP-SQQVMT
          NLVSMTVEGP.PKDTGIA.V.LAGAA.GPGI.RAAGRGIPAGVPMPQAPAGLAGPV.RGVGGP...Q.M.
Retrocopy NLVSMTVEGPLPKDTGIA*VALAGAAVGPGISRAAGRGIPAGVPMPQAPAGLAGPV<RGVGGP<ISQQMM

Parental  PQGRGTVAAAAAA-ATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGPPMGLPPGRGTP
          ........AAA.A.ATASIAGAPTQYPPG.G...PP.G...PP.GM..PP.G..PPM..P....PGRGT.
Retrocopy TPQGRGTVAAAVAAATASIAGAPTQYPPGHGA--PPSGMVGPPLGMW-PPIG--PPMELP----PGRGTL

Parental  MGMPPPGMRPPPPG
          M.MPPPGM.PPPPG
Retrocopy MAMPPPGMWPPPPG

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	0.00 RPM	36.68 RPM
SRP007412_cerebellum	0.00 RPM	37.69 RPM
SRP007412_heart	0.03 RPM	45.67 RPM
SRP007412_kidney	0.00 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_554 was not detected

EST

No EST(s) were mapped for retro_mmus_554 retrocopy.

TSS

No TSS is located nearby retro_mmus_554 retrocopy 5' end.

Lab

retro_mmus_554 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_554 has 0 orthologous retrocopies within eutheria group .

---

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,