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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttccttttccaaattttgaagttaccgtttgtgtgctaggtcttttctcctatccaattcagtgttttatcctagtacatttctcttattcatctaatcttatgctctttgtactttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAGGACAAACACCCCATAAGGGTCAGAGCACCCGTTTAAACAGAATGATGAG

Basic information

species Oryza sativa
transcript LOC_Os05g36110.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g36110.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G073415_T03 (Zea mays), 3'ss of exon 7
gttggttccttttccaaattttgaagttaccgtttgtgtgctaggtcttttctcctatccaattcagtgttttatcctagtacatttctcttattcatctaatcttatgctctttgtactttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAGGACAAACACCCCATAAGGGTCAGAGCACCCGTTTAAACAGAATGATGAG---
                            || |  | | ||||  || ||||||     | ||   |        ||   ||  | |  || ||  ||  |||| |  |     |||| | |  ||||||||| |||||||| ||||||||||| ||||| ||||||||  |  |||  | || |||||| |  ||| | ||   |  ||||||| ||||| ||| ||    
--------------------------caactgaat-tatgctcagtgttttcttggcccgaagctaaaacaaattcaccgtcgactcatcataa-cacttaatatattttctgttgtgcatgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCACAGGTGATCACGTCACTGGAACCAACACCTCGGAAGAGCCA---CGTCCGTTTAGACAGAGTGAGGACTGT

upper sequence: LOC_Os05g36110.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G052855_T01 (Zea mays), 3'ss of exon 6
gttggttccttttccaaattttgaagttaccgtttgtgtgctaggtcttttctcctatccaattcagtgttttatcctagtacatttctcttattcatctaatcttatgctctttgtactttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAGGACAAACACCCCATAAGGGTCAGAGCACCCGTTTAAACAGAATGATGAG
                   |   ||| |||   ||   || |      ||  || || | | ||||      |||  | |    ||  ||| ||      | | || ||||   ||| | |  ||||||||| |||||||| ||||||||||| ||||||||||||||     |||  | || |||||| |  ||| | |||| |  ||||||  ||||| ||| || 
---------------ttggtccaaagctacaaattcattgttga----ttcatcataac-acttca------tatatttgctggttattctaatctgatgatttttctgctg--tgtgcgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGGAACCAACACCTCGGAAGAGCCAGAACGTCCGTTTGGACAGAGTGAGGAC

upper sequence: LOC_Os05g36110.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA04G39490.1 (Glycine max), 3'ss of exon 6
gttggttccttttccaaattttgaagttaccgtttgtgtgctaggtcttttctcctatccaattcagtgttttatcctagtacatttctcttattcatctaatct-tatgctctttgtactttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAGGACAAACACCCCATAAGGGTCAGAGCACCCGTTTAAACAGAATGATGAG
                  ||   |  ||  ||||||  | ||   | ||       || |   | |   | ||||  |    |||||||  || |  | |  | |  |||   ||||    |  | |||||||||||||||| ||||||||||| ||||| ||| ||||  |  ||   | |       | |    |  | | ||   |  ||| ||||||||      
------------------ttagaactttgtcgtttggcttctgcatgtt----gaaattc---ttaaaatattatttt----catttcttctaattttatggtgtacatgtcttttgatgctgatgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGGAAAGGGACACTCGACCGAATGAAAGAGTCTCTTTGAACAGAATTGGATA

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|29621890|gb|CB626901.1|CB626901
EST:     TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAG                         AAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
genomic: TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAGgttggttcct ... ctttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
EST: gi|27576459|gb|CA999153.1|CA999153
EST:     TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAG                         AAATCATTGTTTCTGGAGGAATGACCATGCCGCATGTGATTGCAGCACCAG
genomic: TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAGgttggttcct ... ctttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
EST: gi|29657649|gb|CB653924.1|CB653924
EST:     TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAG                         AAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
genomic: TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAGgttggttcct ... ctttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
EST: gi|66922990|gb|CX109838.1|CX109838
EST:     TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAG                         AAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
genomic: TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAGgttggttcct ... ctttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
EST: gi|88980985|gb|CI021112.1|CI021112
EST:     TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAG                         AAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
genomic: TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAGgttggttcct ... ctttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
EST: gi|58687377|gb|CK076064.1|CK076064
EST:     TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAG                         AAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
genomic: TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAGgttggttcct ... ctttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
EST: gi|88346159|gb|CI634032.1|CI634032
EST:     TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAG                         AAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
genomic: TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAGgttggttcct ... ctttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
EST: gi|86601840|gb|CI258516.1|CI258516
EST:     TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAG                         AAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
genomic: TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAGgttggttcct ... ctttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
EST: gi|86522901|gb|CI163107.1|CI163107
EST:     TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAG                         AAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
genomic: TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAGgttggttcct ... ctttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
EST: gi|29621930|gb|CB626941.1|CB626941
EST:     TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAG                         AAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
genomic: TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAGgttggttcct ... ctttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
EST: gi|86836721|gb|CI347348.1|CI347348
EST:     TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAG                         AAATCATTGTTTCTGGAGGAATGACCATGCCCCAGGTGATTGCAGCACCAG
genomic: TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAGgttggttcct ... ctttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
EST: gi|86423011|gb|CI060584.1|CI060584
EST:     TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAG                         AAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG
genomic: TAGGTCTGAGGAGATTATAAGGCCGAATTTGTCCATTCGAGAAGGGATAGgttggttcct ... ctttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcctagtacatttctcttattcatctaatcttatgctctttgtactttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAGGACAAACACCCCATAAGGGTCAGAGCACCCGTTTAAACAGAATGATGAG
                       atctaat  putative branch site (score: 3)
                                    ctctttgtacttttt  putative PPT
                          taatcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttccttttccaaattttgaagttaccgtttgtgtgctaggtcttttctcctatccaattcagtgttttatcctagtacatttctcttattcatctaatcttatgctctttgtactttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAGGACAAACACCCCATAAGGGTCAGAGCACCCGTTTAAACAGAATGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA