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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacctgatgtttcagtcttgtagatcgttgttgaaaaacatgtgaaaattgtacttacctgaagaattggtggtctgcag

Basic information

species Oryza sativa
transcript LOC_Os08g33440.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g33440.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G117786_T01 (Zea mays), 5'ss of exon 3
TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc----------tgatgtttca--gtcttgtagatcgttgttgaaaaacatgtgaaaattgtacttacctgaagaattggtggtctgcag
 ||||||| ||||||||||| ||||| |||||||| |||||||||||||| |||||||||||||||||||||||||| |||| ||||||||||||||           ||   || ||  || |  ||| | ||  ||||||| |   ||  ||   | |||||||||||| || ||  | |||||
CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaactcatgggctcatggcattgcatagtgtattaggttgtctttgaaaatctcatgtgaac-atgcttacctgaagattttgttatttgcag

upper sequence: LOC_Os08g33440.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G058702_T01 (Zea mays), 5'ss of exon 3
TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc--tgatgtttca--gtcttgtagatcgttgttgaaaaacatgtgaaaattgtacttacctgaagaattggtggtctgcag
 ||||||||||||||||||| ||||| |||||||| ||||| |||||||| || ||||||||||||||||||||||||||||||||||||||||||    ||   || ||  || |  ||||| |   ||| ||| | | |   ||   | |||||||||||| |      | |||||
CTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaattcatggcattgcatagtgtattagattgcctttgcaaatcttctatgaac-atgcttacctgaagatt-----atttgcag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86498267|gb|CI140900.1|CI140900
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|86502788|gb|CI145421.1|CI145421
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|58585893|gb|CF984201.1|CF984201
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|88740335|gb|CI763843.1|CI763843
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|86499821|gb|CI142454.1|CI142454
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|86493670|gb|CI136303.1|CI136303
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|88248712|gb|CI248561.1|CI248561
EST:     GTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: GTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|27920911|gb|CB096719.1|CB096719
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|86497312|gb|CI139945.1|CI139945
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|86501999|gb|CI144632.1|CI144632
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|86504362|gb|CI146995.1|CI146995
EST:     GTCCAAGAAAGCTCGTGCAAAACAGCTCCAACCACATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: GT-CAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|86858948|gb|CI275150.1|CI275150
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|29663234|gb|CB659509.1|CB659509
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTTTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|86597928|gb|CI276714.1|CI276714
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|86499205|gb|CI141838.1|CI141838
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|86501092|gb|CI143725.1|CI143725
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|88224230|gb|CI224079.1|CI224079
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|86504817|gb|CI147450.1|CI147450
EST:     ACAGCTCCAACCCAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: ACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|66912791|gb|CX099639.1|CX099639
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|86503803|gb|CI146436.1|CI146436
EST:     CTCCAACCACATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: CTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|58688879|gb|CK077566.1|CK077566
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGA
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGA
EST: gi|86493073|gb|CI135706.1|CI135706
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|86501837|gb|CI144470.1|CI144470
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
EST: gi|86859001|gb|CI276951.1|CI276951
EST:     AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG
genomic: AGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 71 (upstream exon), 73 (downstream exon)
Score: 38

TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacc ... tggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaacctgatgtttcagtcttgtagatcgttgttgaaaaacatgtgaaaattgtacttacctgaagaattggtggtctgcag

- - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC