RetrogeneDB ID: retro_mmus_2570

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:57460157..57460789(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Snap23
• Ensembl ID: ENSMUSG00000027287
• Aliases: Snap23, 23kDa, AA408749, SNAP-23, Sndt, Syndet
• Description: synaptosomal-associated protein 23 [Source:MGI Symbol;Acc:MGI:109356]

Sequence

>retro_mmus_2570
ATGGATAATCTGTCACCAGAAGAAATTCAGCTGCGGGCTCACCAGGTTACTGATGAGTCAATGGAAAGCACAAGTAGAAT
CCTGGGTTTAGCCATTGAGTCTCAGGATGCAGGAATCAAGACTATCACTATGCTGGAAGACCAAGGGGAACAACTAAATC
ACTTAGAAGAAGACATGGACCAAATAAATTAAGACATGAGAGAGGCAGAGAAGACTTTAACAGAACCCAACAAGTGTTGT
GGCCTCTGAGTCTGCCCTTGTAATAGGACAAAGAAATTTGAGTCTGGAAAGAACTATAAGGCAACATGGGGAGATGGTGG
TGACAACTCACCTAGCAGTATGTAGTATCTAAGCAACCGAGCCTGATAACAAATGGTCAGCCTCAGCAAAATACAGGAGC
AGCCGGTGGTGGATACAGTAAACGTATAACTCATGATGCCAGAGAAGATGAGATGGATGAGAACCTGACTCAAGTGGGCA
GCCTCCTAGGCATACTAAAGAACATGGCTCTGGATATGGGCAATAAAATTGATGCTCAAAACCAGCAAATACAGAAGATC
ACAGAAAAGGGTGACACCAACAAGAGTGGTATTGACAATGCCAATACAAGAGCAAAGAAACTCATTGATAGC

Alignment

ORF - retro_mmus_2570 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDNLSPEEVQLRAHQVTDESLESTRRILGLAIESQDAGIKTITMLDEQGEQLNRIEEGMDQINKDMREAE
          MDNLSPEE.QLRAHQVTDES.EST.RILGLAIESQDAGIKTITML..QGEQLN..EE.MDQIN.DMREAE
Retrocopy MDNLSPEEIQLRAHQVTDESMESTSRILGLAIESQDAGIKTITMLEDQGEQLNHLEEDMDQIN*DMREAE

Parental  KTLTELNKCCGLCICPCNRTKNFESGKNYKATWGDGGDNSPSNV-VSKQPSRITNGQPQQTTGAASG-GY
          KTLTE.NKCCGL..CPCNRTK.FESGKNYKATWGDGGDNSPS...V.............Q....A.G.GY
Retrocopy KTLTEPNKCCGL*VCPCNRTKKFESGKNYKATWGDGGDNSPSSM<VVSKQPSLITNGQPQQNTGAAGGGY

Parental  IKRITNDAREDEMEENLTQVGSILGNLKNMALDMGNEIDAQNQQIQKITEKADTNKNRIDIANTRAKKLI
          .KRIT.DAREDEM.ENLTQVGS.LG.LKNMALDMGN.IDAQNQQIQKITEK.DTNK..ID.ANTRAKKLI
Retrocopy SKRITHDAREDEMDENLTQVGSLLGILKNMALDMGNKIDAQNQQIQKITEKGDTNKSGIDNANTRAKKLI

Parental  DS
          DS
Retrocopy DS

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	14.18 RPM
SRP007412_cerebellum	0.00 RPM	16.02 RPM
SRP007412_heart	0.00 RPM	43.27 RPM
SRP007412_kidney	0.00 RPM	75.59 RPM
SRP007412_liver	0.00 RPM	34.60 RPM
SRP007412_testis	0.00 RPM	33.48 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2570 was not detected

EST

No EST(s) were mapped for retro_mmus_2570 retrocopy.

TSS

No TSS is located nearby retro_mmus_2570 retrocopy 5' end.

Lab

retro_mmus_2570 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2570 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015685	1 retrocopy	retro_acar_38,
Ailuropoda melanoleuca	ENSAMEG00000015774	1 retrocopy	retro_amel_206,
Bos taurus	ENSBTAG00000005661	2 retrocopies	retro_btau_1622, retro_btau_371,
Canis familiaris	ENSCAFG00000011105	2 retrocopies	retro_cfam_1073, retro_cfam_1780,
Choloepus hoffmanni	ENSCHOG00000006468	3 retrocopies	retro_chof_1, retro_chof_1652, retro_chof_1784,
Cavia porcellus	ENSCPOG00000003638	1 retrocopy	retro_cpor_862,
Felis catus	ENSFCAG00000013387	1 retrocopy	retro_fcat_1114,
Loxodonta africana	ENSLAFG00000005462	1 retrocopy	retro_lafr_839,
Microcebus murinus	ENSMICG00000000813	2 retrocopies	retro_mmur_1188, retro_mmur_377,
Monodelphis domestica	ENSMODG00000017889	1 retrocopy	retro_mdom_1772,
Mustela putorius furo	ENSMPUG00000009856	3 retrocopies	retro_mputfur_1181, retro_mputfur_692, retro_mputfur_915,
Mus musculus	ENSMUSG00000027287	1 retrocopy	retro_mmus_2570 ,
Rattus norvegicus	ENSRNOG00000050552	2 retrocopies	retro_rnor_1505, retro_rnor_2389,
Tarsius syrichta	ENSTSYG00000006589	2 retrocopies	retro_tsyr_1020, retro_tsyr_715,
Tursiops truncatus	ENSTTRG00000002561	1 retrocopy	retro_ttru_658,