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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggcgctctctctctctctctctcccttgaacacccatgtgtgcgtgttttggtggatatgtcagtcatggtgcgcaattgaaatttacatttttcctaaatgttacagGTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCG

Basic information

species Oryza sativa
transcript LOC_Os10g11140.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g11140.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 19
gttggcgctctctctctctctctctcccttgaacacccatgtgtgcgtgttttggtggatatgtcagtcatggtgcgcaattgaaatttacatttttcctaaatgttacagGTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCG
      |     |||   ||||||| ||     | ||| ||  || |||   ||   |  ||                     ||||   | |||| | |  || | |||||| || ||||| || ||||| |||||||| ||||||||||| ||||| ||||||||||||||||||||||| ||||||
------gtatgatctgcttctctcttcc----gctcccctgcatgtgtgaaatgaatggcat---------------------aaatcacccttttgcttccatatcacagGTAGACGGTAGTACGGTATCAAAACAAGGACTTCGATTTGTTTTCACTGATGGATCTAGGATTATCTTCCGGCTTTCG
















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|89198777|gb|CI003514.1|CI003514
EST:     GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG                         GTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
genomic: GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCGgttggcgctc ... aatgttacagGTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
EST: gi|24468665|gb|CA305614.1|CA305614
EST:     GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG                         GTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
genomic: GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCGgttggcgctc ... aatgttacagGTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
EST: gi|24468739|gb|CA305688.1|CA305688
EST:     GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG                         GTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
genomic: GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCGgttggcgctc ... aatgttacagGTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
EST: gi|88849912|gb|CI001618.1|CI001618
EST:     GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG                         GTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
genomic: GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCGgttggcgctc ... aatgttacagGTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
EST: gi|44665107|gb|CR278541.1|CR278541
EST:     CCGATGATTTCAGTTACACTGATCCG                         GTGGATGTTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
genomic: CCGATGATTTCAGTTACACTGATCCGgttggcgctc ... aatgttacagGTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
EST: gi|86892654|gb|CI312043.1|CI312043
EST:     GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG                         GTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
genomic: GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCGgttggcgctc ... aatgttacagGTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
EST: gi|86257302|gb|CI004120.1|CI004120
EST:     CCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG                         GTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
genomic: CCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCGgttggcgctc ... aatgttacagGTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
EST: gi|58611262|gb|CK038974.1|CK038974
EST:     GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG                         GTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
genomic: GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCGgttggcgctc ... aatgttacagGTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
EST: gi|44665085|gb|CR278519.1|CR278519
EST:     GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG                         GTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
genomic: GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCGgttggcgctc ... aatgttacagGTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
EST: gi|86503671|gb|CI146304.1|CI146304
EST:     GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG                         GTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
genomic: GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCGgttggcgctc ... aatgttacagGTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
EST: gi|29681951|gb|CB678226.1|CB678226
EST:     GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG                         GTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
genomic: GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCGgttggcgctc ... aatgttacagGTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
EST: gi|86498572|gb|CI141205.1|CI141205
EST:     ATGGAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG                         GTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT
genomic: ATGGAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCGgttggcgctc ... aatgttacagGTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatatgtcagtcatggtgcgcaattgaaatttacatttttcctaaatgttacagGTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCG
                                        tcctaaa  putative branch site (score: 2)
                           aaatttacatttttcc  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggcgctctctctctctctctctcccttgaacacccatgtgtgcgtgttttggtggatatgtcagtcatggtgcgcaattgaaatttacatttttcctaaatgttacagGTGGATGGTAGCACTGTATCTAAACAAGGGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA