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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCAGCAAAGAACTTCGAGATTGCAAGGCTATCCGATAGGGTCCAGTACTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcctgaacttaaacattgatttttgcaattagtacatatgttatgtgtatattattcgtcaatcacaatgcttctttttctgaccttaatccc...

Basic information

species Oryza sativa
transcript LOC_Os02g47580.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47580.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G097738_T01 (Zea mays), 5'ss of exon 3
ATTGCAGCAAAGAACTTCGAGATTGCAAGGCTATCCGATAGGGTCCAGTACTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcctgaacttaaacattgatttttgcaattagtacatatgttatgtgtatattattcgtcaatcacaatgcttctttttctgaccttaatccc---
|||||  |||||||||| ||||||| |||||| || ||||||||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||||| | | | |   |   |    | |||| || |  ||  | | ||||  |   |  |||| | ||  |  ||  ||   ||  | |   | ||| ||     
ATTGCGACAAAGAACTTTGAGATTGGAAGGCTGTCGGATAGGGTCCAGTACTATGAAGCTGCAAACAGGGAAATGTCTCAAAGAAACCAAGAAGCTATCGgtaattacctttcccaccagaggttatttctgta-ctacaaaaaatgtccttgatg-attacttgttgaa-acggtgaccctcatcccctctttattcaaatg

upper sequence: LOC_Os02g47580.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AC202567.4_FGT004 (Zea mays), 5'ss of exon 7
ATTGCAGCAAAGAACTTCGAGATTGCAAGGCTATCCGATAGGGTCCAGTACTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcctgaacttaaacattgatttttgcaattagtacatatgttatgtgtatattattcgtcaatcacaatgcttctttttctgaccttaatccc---
||||| |||||||||||||||||||||||||| || ||||||||||||||||||||||||||||| ||||| ||||| |||||||||||||| ||||||||||   |   |   | |    ||||  |     | |||   ||   || || | | ||       | |     | |  | || |||   ||  | |  ||   
ATTGCCGCAAAGAACTTCGAGATTGCAAGGCTGTCGGATAGGGTCCAGTACTATGAAGCTGCAAATAGGGAAATGTCCCAAAGAAACCAAGAAGCTATCGgtaaatactttctccattgcaattggct---atatttatatcagtggtcatttttgtacagaagatgaccttgattaatactatttgaaacagttacacccct

upper sequence: LOC_Os02g47580.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G046909_T01 (Zea mays), 5'ss of exon 3
ATTGCAGCAAAGAACTTCGAGATTGCAAGGCTATCCGATAGGGTCCAGTACTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcctgaacttaaacattgatttttgcaattagtacatatgtt-atgtgtatattattcgtcaatcacaatgcttctttttctgaccttaatccc---
|||||  ||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||| ||||| |||||||||||||| ||||||||||   |   |   | |    ||||  | |    |||  ||    || | || | | ||       | |     |||  | || |||   ||  |||  ||   
ATTGCCACAAAGAACTTCGAGATTGCAAGGCTGTCGGATAGGGTCCAGTACTATGAAGCTGCAAACAGGGAAATGTCCCAAAGAAACCAAGAAGCTATCGgtaaatactttctccattgcaattggctat----atttatatcagtgctcatttttgtacagaagatgaccttgaataatactatttgaaacggtaacacccct

upper sequence: LOC_Os02g47580.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G107128_T01 (Zea mays), 5'ss of exon 1
ATTGCAGCAAAGAACTTCGAGATTGCAAGGCTATCCGATAGGGTCCAGTACTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcctgaacttaaacattgatttttgcaattagtacatatgttatgtgtatattattcgtcaatcacaatgcttctttttctgaccttaatccc
||||| |||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||| ||||| |||||||||||||| ||||||||||   |   |   | |    ||||  | |    || |  |    | || | |||| |                                          
ATTGCCGCAAAGAACTTCGAGATTGCAAGGCTGTCGGATAGGGTCCAGTACTATGAAGCTGCAAACAGGGAAATGTCCCAAAGAAACCAAGAAGCTATCGgtaaatactttctccattgcaattggctatatttat-atcagtggtcttttttgtacag-----------------------------------------

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|29683032|gb|CB679307.1|CB679307
EST:     CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCG                         AGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
genomic: CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcc ... tgtcttgcagAGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
EST: gi|218498673|gb|FG952682.1|FG952682
EST:     CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCG                         AGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
genomic: CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcc ... tgtcttgcagAGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
EST: gi|86601924|gb|CI258600.1|CI258600
EST:     CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCG                         AGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
genomic: CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcc ... tgtcttgcagAGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
EST: gi|86827872|gb|CI274821.1|CI274821
EST:     CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCG                         AGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
genomic: CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcc ... tgtcttgcagAGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
EST: gi|218485961|gb|FG956965.1|FG956965
EST:     CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCG                         AGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
genomic: CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcc ... tgtcttgcagAGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
EST: gi|58605335|gb|CK033368.1|CK033368
EST:     CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCG                         AGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
genomic: CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcc ... tgtcttgcagAGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
EST: gi|33676196|gb|CF304435.1|CF304435
EST:     CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCG                         AGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
genomic: CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcc ... tgtcttgcagAGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
EST: gi|58688624|gb|CK077311.1|CK077311
EST:     CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCG                         AGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
genomic: CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcc ... tgtcttgcagAGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
EST: gi|86496876|gb|CI139509.1|CI139509
EST:     CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCG                         AGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
genomic: CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcc ... tgtcttgcagAGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
EST: gi|88508406|gb|CI435912.1|CI435912
EST:     CTATGAAGCTGCAAACAGGGAGATTTCTCAAAGAAACCAAGAGGCTATCG                         AGATGTCGAGGCAACAACGAAATATCCGAAAGGAGAGACAGAAGTGGTTGT
genomic: CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcc ... tgtcttgcagAGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
EST: gi|218494793|gb|FG959706.1|FG959706
EST:     TATGAAGCTGGCAAACAGGGAGATGTCTCAAAGCAACCAAGAGGCTATCG                         AGATGTCGAGGCAACAACGACATATCCGAAAGAAGAGACAGAAGTG
genomic: TATGAAGCTG-CAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcc ... tgtcttgcagAGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTG
EST: gi|88250834|gb|CI248685.1|CI248685
EST:     CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCG                         AGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
genomic: CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcc ... tgtcttgcagAGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
EST: gi|29664963|gb|CB661238.1|CB661238
EST:     CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCG                         AGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT
genomic: CTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcc ... tgtcttgcagAGATGTCGAGGCAACAACGAAATATCCGAAAGAAGAGACAGAAGTGGTTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGCAGCAAAGAACTTCGAGATTGCAAGGCTATCCGATAGGGTCCAGTACTATGAAGCTGCAAACAGGGAGATGTCTCAAAGAAACCAAGAGGCTATCGgtactcatcctgaacttaaacattgatttttgcaattagtacatatgttatgtgtatattattcgtcaatcacaatgcttctttttctgaccttaatccc

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG