RetrogeneDB ID: retro_mmus_1307

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:105199978..105201101(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lcp1
• Ensembl ID: ENSMUSG00000021998
• Aliases: Lcp1, AW536232, D14Ertd310e, LCP-1, Pls2, pp65
• Description: lymphocyte cytosolic protein 1 [Source:MGI Symbol;Acc:MGI:104808]

Sequence

>retro_mmus_1307
GCAGAGACAGATACCGATGGCAACGGATACATCAGCTACAATGAGCTGCGTCACTTGTTCAAGGCCGCCTGCTGGCCTCT
GCCTGGGTACCGAGTGAGAGAAATTGCAGAAACCTGATGGCCACAGGTGATCTGGACCAAGATAGAAAGATAAAGCTTTG
ATGAGTTTATCAAGGTCTTCCATGGCTTAAAAAGCACCGAGGTTGCCAAAACCTTCCAAAAAAGCTATCAACAAGAAAAA
AGATCTGTGCAATTGGCGGCACCTCTGAGCAGTCTAGTGTTGGTACCCAGCACTCTTATTCAGAGGAAGAAAAGTATGCC
TTAGTCAACTGGATAAACAAAGCCCTGGAGAATGATCTCGACTGCCGGCACGTCATCCCCATGAACCCCAACACCGACGA
TCTCTTCAATGCTGTAGGCGTTGGCATAGTTCTTTGTAAAATGATCAACCTGTCCGTGCCAGACACAATTGACGAGAGAA
CGATCAACAAGAAAAAGCTCACACCGTTCACCATTCGGGAAAACTTGAACTTGACTCTGAACTCTGCCTTGGCCATCGGG
TGCCACGTGGTTAATATAGGGGCCGAGGACCTGAAGGAGGGCAAGCCTTACCTGGTCCTGGGACTTCTGTGGCAAGTCAT
CAAGATTGGGTTGTTTGTTGACATTGAACTCAGCAGAAATGAAGCTCTGATTGCTCTTTTGAGAGAAGGAGAGAGCCTAG
AGGATTTGATGAAGTTGTCTCCTGAAGAATTCCTGCTGCAGTGGGCTAACTACCACCTAGAAAACGCAGGCTGCACCAAA
ATCACCAACTTCAGCACGACATCAAGGACTCCAAAGCTTATTACCACCTGCTCGAGCAAGTGGCTCCAAAAGGAGATGAA
GAAGGGATCCCGGCTGTTGTGATTGACACATCAGGACTGAAGAAGGATGACATCCAGAGTGCAGAGCGCATGCTGCAACA
GGCGGAGAGGCTGGGCTGCCGGCAGTTTGTCACAGCTACTGATGTTGTCCGAGGGAACCCCAAGTTGAACCTGGTCTTCA
TTGCCAACCTCTTTAACAAATACCCTGCCTTACATAAACCAGAGAACCAGGACATTGACTGGGGGGCTCTCGAAGAGCGG
ACG

Alignment

ORF - retro_mmus_1307 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.26 %
• Parental protein coverage: 59.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AKVDTDGNGYISCNELNDLFKAACLPLPGYRVREITE-NLMATGDLDQDGKI-SFDEFIKVFHGLKSTEV
          A..DTDGNGYIS.NEL..LFKAAC.PLPGYRVREI.E.NLMATGDLDQD.KI.SFDEFIKVFHGLKSTEV
Retrocopy AETDTDGNGYISYNELRHLFKAACWPLPGYRVREIAE<NLMATGDLDQDRKI>SFDEFIKVFHGLKSTEV

Parental  AKTFRKA-INKKEGICAIGGTSEQSSVGTQHSYSEEEKYAFVNWINKALENDPDCRHVIPMNPNTDDLFN
          AKTF.K........ICAIGGTSEQSSVGTQHSYSEEEKYA.VNWINKALEND.DCRHVIPMNPNTDDLFN
Retrocopy AKTFQKS<LSTRKKICAIGGTSEQSSVGTQHSYSEEEKYALVNWINKALENDLDCRHVIPMNPNTDDLFN

Parental  AVGDGIVLCKMINLSVPDTIDERTINKKKLTPFTIQENLNLALNSASAIGCHVVNIGAEDLKEGKPYLVL
          AVG.GIVLCKMINLSVPDTIDERTINKKKLTPFTI.ENLNL.LNSA.AIGCHVVNIGAEDLKEGKPYLVL
Retrocopy AVGVGIVLCKMINLSVPDTIDERTINKKKLTPFTIRENLNLTLNSALAIGCHVVNIGAEDLKEGKPYLVL

Parental  GLLWQVIKIGLFADIELSRNEALIALLREGESLEDLMKLSPEELLLRWANYHLENAGCTKITNFST-DIK
          GLLWQVIKIGLF.DIELSRNEALIALLREGESLEDLMKLSPEE.LL.WANYHLENAGCTKITNFST.DIK
Retrocopy GLLWQVIKIGLFVDIELSRNEALIALLREGESLEDLMKLSPEEFLLQWANYHLENAGCTKITNFST<DIK

Parental  DSKAYYHLLEQVAPKGDEEGIPAVVIDMSGLREKDDIQRAECMLQQAERLGCRQFVTATDVVRGNPKLNL
          DSKAYYHLLEQVAPKGDEEGIPAVVID.SGL..KDDIQ.AE.MLQQAERLGCRQFVTATDVVRGNPKLNL
Retrocopy DSKAYYHLLEQVAPKGDEEGIPAVVIDTSGLK-KDDIQSAERMLQQAERLGCRQFVTATDVVRGNPKLNL

Parental  AFIANLFNKYPALHKPENQDIDWGALEGET
          .FIANLFNKYPALHKPENQDIDWGALE..T
Retrocopy VFIANLFNKYPALHKPENQDIDWGALEERT

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	7.85 RPM
SRP007412_cerebellum	0.04 RPM	10.64 RPM
SRP007412_heart	0.00 RPM	26.31 RPM
SRP007412_kidney	0.06 RPM	49.03 RPM
SRP007412_liver	0.00 RPM	88.45 RPM
SRP007412_testis	0.05 RPM	2.65 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1307 was not detected

EST

No EST(s) were mapped for retro_mmus_1307 retrocopy.

TSS

No TSS is located nearby retro_mmus_1307 retrocopy 5' end.

Lab

retro_mmus_1307 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1307 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012037	1 retrocopy	retro_chof_1057,
Mus musculus	ENSMUSG00000021998	2 retrocopies	retro_mmus_1307 , retro_mmus_3697,