RetrogeneDB ID: retro_mmus_814

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:65037051..65037498(-)
• Located in intron of: ENSMUSG00000033389

Retrocopy information

• Ensembl ID: ENSMUSG00000083935
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Taf9
• Ensembl ID: ENSMUSG00000078941
• Aliases: Ak6, 2810046E22Rik, 4921516M08Rik, AK/ATPase
• Description: TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor [Source:MGI Symbol;Acc:MGI:1888697]

Sequence

>retro_mmus_814
AAAACAGGACTGAAGTACAAAAATGTGGCTGATTTAGCTCCAGGAGGGCAGGTTTTTATATGATGGCTATGATGAATAAT
ATGATTGTCTCATTTTAGATAATGATAGAGCTGTTGATGAGTTAGAGAGTCAGATGAGACAAGGCAGGATTATTGTTGAT
TACTGTGGTTATGAGTCCTTTCCTGAACACTGAATTCATATAGTGTTTGTATTCAGAAGTAATGGTATATTGTTAAAAAA
AAAAAAAGACTTGAAACAAGGGGGGTTAATGAGGAGAGAATACAAGACAGGATTCAGTGTGAGAGTTTTCAAGTTCTTTA
TGAAGAAGCCATAGCATCTTACAAAGAAGAAATTGTGCATCCACTACCCAATAATGAACTAGAAGAATTAAATGATAATG
TCAACTTAATCACAAAATGGATTGGGCAATGGGTCAAGGATAACAAC

Alignment

ORF - retro_mmus_814 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.55 %
• Parental protein coverage: 84.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSGLKYVNVGDLA-REGQ-LYDGYDEEYGCPILDEDRVVDELEHQMQEGGVIVDYHGCDFFPERWFHIVF
          ..GLKY.NV.DLA..EG..LYDGYDE.Y.C.ILD.DR.VDELE.QM..G..IVDY.G...FPE...HIVF
Retrocopy KTGLKYKNVADLA>QEGRFLYDGYDE*YDCLILDNDRAVDELESQMRQGRIIVDYCGYESFPEH*IHIVF

Parental  VLRTDNGVLYKR---LETRGYNEKKLQDNIQCEIF-QVLYEEAIASYKEEIVHQLPSNEPEQLEDNINQI
          V.R..NG.L......L...G..............F.QVLYEEAIASYKEEIVH.LP.NE.E.L.DN.N.I
Retrocopy VFRS-NGILXXXXXDLKQGGLMRREYKTGFSVRVF<QVLYEEAIASYKEEIVHPLPNNELEELNDNVNLI

Parental  SKWIEQWVKDHN
          .KWI.QWVKD.N
Retrocopy TKWIGQWVKDNN

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	0.07 RPM	5.96 RPM
SRP007412_cerebellum	0.22 RPM	6.21 RPM
SRP007412_heart	0.09 RPM	6.57 RPM
SRP007412_kidney	0.02 RPM	10.49 RPM
SRP007412_liver	0.00 RPM	6.20 RPM
SRP007412_testis	0.00 RPM	13.49 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_814 was not detected

EST

No EST(s) were mapped for retro_mmus_814 retrocopy.

TSS

No TSS is located nearby retro_mmus_814 retrocopy 5' end.

Lab

retro_mmus_814 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_814 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012471	4 retrocopies	retro_chof_1120, retro_chof_1976, retro_chof_734, retro_chof_84,
Callithrix jacchus	ENSCJAG00000036421	1 retrocopy	retro_cjac_3025,
Dasypus novemcinctus	ENSDNOG00000024524	3 retrocopies	retro_dnov_1274, retro_dnov_2010, retro_dnov_398,
Gorilla gorilla	ENSGGOG00000015545	1 retrocopy	retro_ggor_864,
Macropus eugenii	ENSMEUG00000016022	12 retrocopies	retro_meug_1043, retro_meug_132, retro_meug_134, retro_meug_1480, retro_meug_1547, retro_meug_1622, retro_meug_284, retro_meug_332, retro_meug_364, retro_meug_427, retro_meug_722, retro_meug_897,
Myotis lucifugus	ENSMLUG00000028932	4 retrocopies	retro_mluc_1134, retro_mluc_1330, retro_mluc_1661, retro_mluc_458,
Monodelphis domestica	ENSMODG00000019421	14 retrocopies	retro_mdom_1016, retro_mdom_1136, retro_mdom_1204, retro_mdom_1430, retro_mdom_1826, retro_mdom_1827, retro_mdom_2023, retro_mdom_409, retro_mdom_459, retro_mdom_519, retro_mdom_55, retro_mdom_666, retro_mdom_845, retro_mdom_913,
Mustela putorius furo	ENSMPUG00000014588	1 retrocopy	retro_mputfur_830,
Mus musculus	ENSMUSG00000078941	2 retrocopies	retro_mmus_3717, retro_mmus_814 ,
Nomascus leucogenys	ENSNLEG00000004086	2 retrocopies	retro_nleu_2237, retro_nleu_2670,
Oryctolagus cuniculus	ENSOCUG00000020970	1 retrocopy	retro_ocun_6,
Otolemur garnettii	ENSOGAG00000027736	4 retrocopies	retro_ogar_1080, retro_ogar_2051, retro_ogar_3344, retro_ogar_876,
Pongo abelii	ENSPPYG00000015527	3 retrocopies	retro_pabe_3298, retro_pabe_483, retro_pabe_835,
Pan troglodytes	ENSPTRG00000016949	10 retrocopies	retro_ptro_138, retro_ptro_2726, retro_ptro_3286, retro_ptro_3291, retro_ptro_3299, retro_ptro_3301, retro_ptro_3303, retro_ptro_3306, retro_ptro_3308, retro_ptro_761,
Rattus norvegicus	ENSRNOG00000039848	1 retrocopy	retro_rnor_280,
Sarcophilus harrisii	ENSSHAG00000017216	2 retrocopies	retro_shar_451, retro_shar_511,
Ictidomys tridecemlineatus	ENSSTOG00000024448	2 retrocopies	retro_itri_1475, retro_itri_995,