RetrogeneDB ID: retro_mmus_2353

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:53662295..53662975(+)
• Located in intron of: ENSMUSG00000054752

Retrocopy information

• Ensembl ID: ENSMUSG00000081516
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ssbp2
• Ensembl ID: ENSMUSG00000003992
• Aliases: Ssbp2, 1500004K09Rik, 2310079I02Rik, 9330163K02Rik, A830008M03Rik, AU067692, AW558684, Hspc116, SSDP2
• Description: single-stranded DNA binding protein 2 [Source:MGI Symbol;Acc:MGI:1914220]

Sequence

>retro_mmus_2353
ATGTACAGCAAAGGCAGCAGTTAACAGCAGTGCGCCCCGTGCAGCAGCCAGGCCAGGGGGAGTCAGCACTGCGTGTATGG
ATGTCTGCTTCATGTAGGCACTCAGAAATAGGCTCAGACATTTTTATCAGAGATAAGATGGGAAAAAAACATCACATTGG
GGGGGAGGGCAGGATTCTTACATTCTTGGTGGTGTGTGTTTTGGGATTTCTACTGTGCAGCTCCAGAGAGACGGGAACAC
TCAAAGCAAAAGCCTTCCATGATTATAGTGCTGCAGCAGCTCCCAGCCCCATGCTAGGAAGCATGCCCCCAGGAGATGGC
ATGCCAATAGGTCCCATGCCACCAGGGTTCTTTTAGCCTTTTATGTCATCTCAGTACCTTGGAGGCCCAAGGCCCCCATT
GAGGATACCTAATCAGGCACTTGGAGGTATCCCAGGAAGTCAGCCATTACACCCCAGTGGAATGGATCCATCATGACAAC
AAGGTCATCCAAATATGGGTGGACCAATGCAGAGAATGACTCCCCCAAGAGGTACGGTGCCCTTAGGACCACAGAACTAT
GGAGGTGCAATGAGACCCCCACTGAATGCTTTAGGTGGCTCTGGAATGCCTGGAATGAACATGGGTCCAGGTGGTGGTAG
ACCTTGGCCAAACCCAACAAATGCCAATTCAATACCCTAC

Alignment

ORF - retro_mmus_2353 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 64.27 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MYGKGKSNSSAVPSDSQAREKLALYVYEYLLHVGAQKSAQTFLSEIRWEKNITLGEPPGFLHS-WW-CVF
          MY.KG.S.....P..SQAR......VY..LLHVG.QK.AQTFLSEIRWEKNITLG...GFLHS.W..CV.
Retrocopy MYSKGSS*QQCAPCSSQARGSQHC-VYGCLLHVGTQK*AQTFLSEIRWEKNITLGGRAGFLHSWWC<CVL

Parental  WDLYCAAPERRETCEHSSEAKAFHDYSAAAAPSPVLGNMPPGDGMPVGPVPPGFFQPFMSPRYPGGPRPP
          ..L.C.....RET......AKAFHDYSAAAAPSP.LG.MPPGDGMP.GP.PPGFF.PFMS..Y.GGPRPP
Retrocopy GFLLCSS---RET--GTLKAKAFHDYSAAAAPSPMLGSMPPGDGMPIGPMPPGFF*PFMSSQYLGGPRPP

Parental  LRIPNQALGGVPGSQPLLPSGMDPTRQQGHPNMGGPMQRMTPPRGMVPLGPQNYGGAMRPPLNALGGPGM
          LRIPNQALGG.PGSQPL.PSGMDP..QQGHPNMGGPMQRMTPPRG.VPLGPQNYGGAMRPPLNALGG.GM
Retrocopy LRIPNQALGGIPGSQPLHPSGMDPS*QQGHPNMGGPMQRMTPPRGTVPLGPQNYGGAMRPPLNALGGSGM

Parental  PGMNMGPGGGRPWPNPTNANSIPY
          PGMNMGPGGGRPWPNPTNANSIPY
Retrocopy PGMNMGPGGGRPWPNPTNANSIPY

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	0.09 RPM	57.94 RPM
SRP007412_cerebellum	0.04 RPM	41.42 RPM
SRP007412_heart	0.06 RPM	18.58 RPM
SRP007412_kidney	0.08 RPM	15.80 RPM
SRP007412_liver	0.03 RPM	0.98 RPM
SRP007412_testis	0.00 RPM	9.56 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2353 was not detected

EST

No EST(s) were mapped for retro_mmus_2353 retrocopy.

TSS

No TSS is located nearby retro_mmus_2353 retrocopy 5' end.

Lab

retro_mmus_2353 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2353 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000145687	1 retrocopy	retro_hsap_3622,
Macaca mulatta	ENSMMUG00000017583	1 retrocopy	retro_mmul_1768,
Mus musculus	ENSMUSG00000003992	1 retrocopy	retro_mmus_2353 ,