RetrogeneDB ID: retro_mmus_433

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:45520243..45520750(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Apex1
• Ensembl ID: ENSMUSG00000035960
• Aliases: Apex1, APE, Apex, HAP1, Ref-1
• Description: apurinic/apyrimidinic endonuclease 1 [Source:MGI Symbol;Acc:MGI:88042]

Sequence

>retro_mmus_433
CAAAGCAGCGGTGAGGACGAGGAAGAACCCACGTCCGAGCCAGAGACCAAGAAGAGTAAGGGGGCAGCAAAGAAAACTGA
GAAGGAAGCCGCAGGAGAGGGCCCTGTCCTGTATGAGGACCCTCCAGATCAGAAAACCTTACCCAGTGGCAAATCTGCCA
CTCTCAAGATATGCTCCTGGAATGTGGATGGGCTTCGAGCCTGCAATAAAAAGAAGGGTTTGGATTGGGTAAAGGTAGAA
GCACCAGATATGTTGTGCCTCCAAGAGACCAAGTGCTCAGAAAACAAACTTCCTCCCGAGCTTCAAGAGCTGCCTGGACT
CACCTATCAGTATTGGTCAGCTCCGTCAGACAAAGAAGGATCCAGTGGTGTGCGCCTACTTTCCTGCCAGTGCCCACTAA
AAGTCTCTTATGGCACTGGTGAGGAAGAACCTGATCAAGAAGGCTGATTGATTGTGGCTGAATTTGAGTCCTTTGTCTTG
GTACCAGCCTATGTTTCCAATACAGGC

Alignment

ORF - retro_mmus_433 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.8 %
• Parental protein coverage: 95.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KAAADDGEEPKSEPETKKSKGAAKKTEKEAAGEGPVLYEDPPDQKTSPSGKSATLKICSWNVDGLRAWIK
          .....D.EEP.SEPETKKSKGAAKKTEKEAAGEGPVLYEDPPDQKT.PSGKSATLKICSWNVDGLRA..K
Retrocopy QSSGEDEEEPTSEPETKKSKGAAKKTEKEAAGEGPVLYEDPPDQKTLPSGKSATLKICSWNVDGLRACNK

Parental  KKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLTHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIG
          KKGLDWVK.EAPD.LCLQETKCSENKLP.ELQELPGLT.QYWSAPSDKEG.SGV.LLS.QCPLKVSYG.G
Retrocopy KKGLDWVKVEAPDMLCLQETKCSENKLPPELQELPGLTYQYWSAPSDKEGSSGVRLLSCQCPLKVSYGTG

Parental  EEEHDQEGRVIVAEFESFVLVTAYVPNAG
          EEE.DQEG..IVAEFESFVLV.AYV.N.G
Retrocopy EEEPDQEG*LIVAEFESFVLVPAYVSNTG

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	3.11 RPM
SRP007412_cerebellum	0.00 RPM	2.04 RPM
SRP007412_heart	0.00 RPM	2.71 RPM
SRP007412_kidney	0.00 RPM	2.44 RPM
SRP007412_liver	0.00 RPM	3.66 RPM
SRP007412_testis	0.00 RPM	4.44 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_433 was not detected

EST

No EST(s) were mapped for retro_mmus_433 retrocopy.

TSS

No TSS is located nearby retro_mmus_433 retrocopy 5' end.

Lab

retro_mmus_433 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_433 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002745	1 retrocopy	retro_btau_1729,
Echinops telfairi	ENSETEG00000004855	1 retrocopy	retro_etel_1392,
Loxodonta africana	ENSLAFG00000021872	1 retrocopy	retro_lafr_948,
Mus musculus	ENSMUSG00000025269	1 retrocopy	retro_mmus_2564,
Mus musculus	ENSMUSG00000035960	2 retrocopies	retro_mmus_2027, retro_mmus_433 ,
Otolemur garnettii	ENSOGAG00000013335	3 retrocopies	retro_ogar_1284, retro_ogar_2145, retro_ogar_3243,
Rattus norvegicus	ENSRNOG00000009663	1 retrocopy	retro_rnor_2971,
Ictidomys tridecemlineatus	ENSSTOG00000010096	1 retrocopy	retro_itri_1560,
Tupaia belangeri	ENSTBEG00000006405	1 retrocopy	retro_tbel_3409,