RetrogeneDB ID: retro_mmus_1111

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:64927939..64928797(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Smarce1
• Ensembl ID: ENSMUSG00000037935
• Aliases: Smarce1, 2810417B20Rik, 5830412H02Rik, 9030408N19Rik, Baf27
• Description: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:MGI Symbol;Acc:MGI:1927347]

Sequence

>retro_mmus_1111
GAGTACAATGAGTCTATGAAGGCCTACCATAATTCCCCTGCGTACCTTGCCTATATTAATGCAAAAAGTCGTGTGGAAGC
TGCATTAGAGGAAGAAAGTCGACAGAGACAGTCTCGCATGGAGAAAGGAGACCCTTACTTGAGCATTCAGCCTGCTGAGG
ATCCAGATGATGATAATGATGGCTTTTCAATGAAGCACACAGCCACTGCCCGTTTCCAGAGAAACCACCGTCTCATCAGT
GAGATCCTCAGTGAGAGTGTGGCACCTGATGTGCGGTCGGTTGTCACGACAGCTAGAATGCAGGTCCTCAAGCGACAGGT
CCAGTCTTTAATGGTTCATCAGCGGAAACTAGAAGCCGAGCTCCTTCAGATAGAGGAACGACACCAGGAAAAGAAGAGGA
AATTCCTGGAAAGCACAGACTCCTTTAACAATGAACTTAAAAGGTTATGTGGTCTGAAGGTGGAAGTAGACATGGAGAAG
ATTGCGGCTGAGATCGCACAGGCGGAGGAACAGGCCCGCAAGAGGCAGGAGGAGAGGGGGAAGGAGGCAGCAGAGCAGGC
TGAGCGCACTCAGAGCAGCATCGCCCCCGAGGAAGAGCAAGTGGCGAACAAAGCCGAGGAGAAGAAGGATGAGGAGAGCA
TCCCAATGGAGACAGAGGAGACACACCTTGAAGACACGGCAGAGAGCCAGCAGAATGGTGAAGAAGGCACGTCTACTCCT
GAGGACAAGGAGAGTGGGCAGGAGGGGGTTGACAGCATGGAGGTGGAAGGGACCAGTGACAGTAACACGGGCTCATAGAG
CAACAGCGCCACAGTGGAGGAGCCGCCCACAGACCCAGTGCCAGAAGACGAGAAGGAG

Alignment

ORF - retro_mmus_1111 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.15 %
• Parental protein coverage: 69.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EYNESMKAYHNSPAYLAYINAKSRAEAALEEESRQRQSRMEKGEPYMSIQPAEDPDDYDDGFSMKHTATA
          EYNESMKAYHNSPAYLAYINAKSR.EAALEEESRQRQSRMEKG.PY.SIQPAEDPDD..DGFSMKHTATA
Retrocopy EYNESMKAYHNSPAYLAYINAKSRVEAALEEESRQRQSRMEKGDPYLSIQPAEDPDDDNDGFSMKHTATA

Parental  RFQRNHRLISEILSESVVPDVRSVVTTARMQVLKRQVQSLMVHQRKLEAELLQIEERHQEKKRKFLESTD
          RFQRNHRLISEILSESV.PDVRSVVTTARMQVLKRQVQSLMVHQRKLEAELLQIEERHQEKKRKFLESTD
Retrocopy RFQRNHRLISEILSESVAPDVRSVVTTARMQVLKRQVQSLMVHQRKLEAELLQIEERHQEKKRKFLESTD

Parental  SFNNELKRLCGLKVEVDMEKIAAEIAQAEEQARKRQEEREKEAAEQAERSQSSMAPEEEQVANKAEEKKD
          SFNNELKRLCGLKVEVDMEKIAAEIAQAEEQARKRQEER.KEAAEQAER.QSS.APEEEQVANKAEEKKD
Retrocopy SFNNELKRLCGLKVEVDMEKIAAEIAQAEEQARKRQEERGKEAAEQAERTQSSIAPEEEQVANKAEEKKD

Parental  EESIPMETEETHLEDTAESQQNGEEGTSTPEDKESGQEGVDSMEVEGTSDSNTGSESNSATVEEPPTDPV
          EESIPMETEETHLEDTAESQQNGEEGTSTPEDKESGQEGVDSMEVEGTSDSNTGS.SNSATVEEPPTDPV
Retrocopy EESIPMETEETHLEDTAESQQNGEEGTSTPEDKESGQEGVDSMEVEGTSDSNTGS*SNSATVEEPPTDPV

Parental  PEDEKK
          PEDEK.
Retrocopy PEDEKE

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	0.05 RPM	25.56 RPM
SRP007412_cerebellum	0.30 RPM	30.70 RPM
SRP007412_heart	0.03 RPM	35.24 RPM
SRP007412_kidney	0.62 RPM	33.34 RPM
SRP007412_liver	0.14 RPM	17.45 RPM
SRP007412_testis	0.87 RPM	35.36 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1111 was not detected

EST

No EST(s) were mapped for retro_mmus_1111 retrocopy.

TSS

No TSS is located nearby retro_mmus_1111 retrocopy 5' end.

Lab

retro_mmus_1111 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1111 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013573	4 retrocopies	retro_cjac_1107, retro_cjac_2109, retro_cjac_50, retro_cjac_854,
Homo sapiens	ENSG00000073584	5 retrocopies	retro_hsap_1195, retro_hsap_1304, retro_hsap_3623, retro_hsap_3947, retro_hsap_922,
Gorilla gorilla	ENSGGOG00000011803	2 retrocopies	retro_ggor_1020, retro_ggor_931,
Microcebus murinus	ENSMICG00000009821	4 retrocopies	retro_mmur_1408, retro_mmur_1592, retro_mmur_608, retro_mmur_928,
Myotis lucifugus	ENSMLUG00000004609	1 retrocopy	retro_mluc_1209,
Macaca mulatta	ENSMMUG00000004005	3 retrocopies	retro_mmul_1284, retro_mmul_2159, retro_mmul_2286,
Mustela putorius furo	ENSMPUG00000014660	4 retrocopies	retro_mputfur_1411, retro_mputfur_1482, retro_mputfur_1499, retro_mputfur_739,
Mus musculus	ENSMUSG00000037935	5 retrocopies	retro_mmus_1111 , retro_mmus_1127, retro_mmus_2437, retro_mmus_2618, retro_mmus_3194,
Nomascus leucogenys	ENSNLEG00000001957	4 retrocopies	retro_nleu_1060, retro_nleu_2051, retro_nleu_2083, retro_nleu_286,
Oryctolagus cuniculus	ENSOCUG00000008981	1 retrocopy	retro_ocun_59,
Otolemur garnettii	ENSOGAG00000001652	7 retrocopies	retro_ogar_1734, retro_ogar_2059, retro_ogar_3199, retro_ogar_402, retro_ogar_454, retro_ogar_682, retro_ogar_760,
Ochotona princeps	ENSOPRG00000000985	1 retrocopy	retro_opri_731,
Pongo abelii	ENSPPYG00000008456	4 retrocopies	retro_pabe_2973, retro_pabe_3251, retro_pabe_794, retro_pabe_994,
Pan troglodytes	ENSPTRG00000022902	5 retrocopies	retro_ptro_2451, retro_ptro_2678, retro_ptro_3039, retro_ptro_639, retro_ptro_894,
Pteropus vampyrus	ENSPVAG00000011355	1 retrocopy	retro_pvam_237,
Rattus norvegicus	ENSRNOG00000010676	7 retrocopies	retro_rnor_1278, retro_rnor_1311, retro_rnor_1456, retro_rnor_1507, retro_rnor_1599, retro_rnor_2383, retro_rnor_2593,
Tupaia belangeri	ENSTBEG00000000770	10 retrocopies	retro_tbel_1246, retro_tbel_1554, retro_tbel_2208, retro_tbel_2955, retro_tbel_4035, retro_tbel_4629, retro_tbel_4656, retro_tbel_658, retro_tbel_821, retro_tbel_844,