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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttcctagaatgttgtccaattctgaagtatgatcagcatgacctttatatgatattgattgtatgaaatttgtgaatctgcagGATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGTGGAATGGGGGGAATGGGAGGCCGTGCTGCTCGGAACAGACCAATGCAGG

Basic information

species Oryza sativa
transcript LOC_Os05g26914.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g26914.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G013934_T01 (Zea mays), 3'ss of exon 6
-----------gtgagtgt-tcctagaatgttgtccaattctgaagtatgatcagcatgacctttatatgatattgattgtatgaaatttgtgaatctgcagGATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGTGGAATGGGGGGAATGGGAGG---CCGTGCTGCTCGGAACAGACCAATGCAGG
| |||| || | || | || ||| ||||| || ||||| || | || || | | || ||| || |||| || ||||||||||||||||| || ||||||||||| || | || ||||| ||||||| |||||| |||||||| || ||||||||||||||||||||||||||
tggaaaacattctaggtgtatcatggattactgaattgttc-gaagtttggtcagcgggatcattgaattgttctaatcatatcaa-tttggtttcctacagGATTACTCAAACCCGTTTGATCTCTTTGAGTCCCTGTTTGAAGGGTTTGGTGAAATGGGTGGAATGGGGGGTGGCCGTGCTGCTCGGAACAGACCAATGC---

upper sequence: LOC_Os05g26914.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G851710_T01 (Zea mays), 3'ss of exon 6
-----------gtgagtgt-tcctagaatgttgtccaattctgaagtatgatcagcatgacctttatatgatattgattgtatgaaatttgtgaatctgcagGATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGTGGAATGGGGGGAATGGGAGG---CCGTGCTGCTCGGAACAGACCAATGCAGG
| |||| || | | | || ||| ||||| || ||||| || | || || | | || ||| || |||| || ||||||||||||||||| || ||||||||||| || | || ||||| ||||||| |||||| |||||||| || ||||||||||||||||| ||||||||
tggaaaacattctaggtgtatcatgaattactgaattgttc-gaagtttggtcagcgggatcattgaattgttctaatcatatcaa-tttggtttcctacagGATTACTCAAACCCGTTTGATCTCTTTGAGTCCCTGTTTGAAGGGTTTGGTGAAATGGGTGGAATGGGGGGTGGCCGTGCTGCTCGGAACATACCAATGC---

upper sequence: LOC_Os05g26914.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G091811_T01 (Zea mays), 3'ss of exon 7
gtgagtgttcctagaatgttgtccaattctgaagtatgatcagcatgacctttatatgatattgattgtatgaaatttgtgaatctgcagGATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGTGGAATGGGGGGAATGGGAGGC---CGTGCTGCTCGGAACAGACCAATGCAGG
|| ||||||| | | || | || | || ||||| || |||||| || | || | | | || | | || ||||| || ||||||||||||||||| || ||||| || || || | || ||||| || ||||| ||||| |||||||| ||| |||||||| || |||||||||||||
gtaagtgttcttcta-tggtttctatatcagaagtttggtcagcaggatccttgatttgttctaatcatgtcaattttgttt-cctacagGATTACTCAAACCCGTTTGATCTATTCGAGTCCCTGTTTGAAGGATTCGGTGGGATGGGTGGAATGGGTGGCGGTCGTGCTGCCCGTAACAGACCAATGC---

upper sequence: LOC_Os05g26914.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G856084_T01 (Zea mays), 3'ss of exon 7
gtgagtgttcctagaatgttgtccaattctgaagtatgatcagcatgacctttatatgatattgattgtatgaaatttgtgaatctgcagGATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGTGGAATGGGGGGAATGGGAGG---CCGTGCTGCTCGGAACAGACCAATGCAGG
|| |||||||||| | |||| || | || ||||| || |||||| || | || || | | || ||| || ||||| || ||||||||||||||||| || ||||||||||| || | || ||||| |||||||||||||| |||||||| || ||||||||||||||||||||||||||
gtaagtgttcctata-tgttttctatatcagaagtttggtcagcaggatcattgaattgttctaatcatatcaattttgttt-cctacagGATTACTCAAACCCGTTTGATCTCTTTGAGTCCCTGTTTGAAGGGTTTGGTGGAATGGGTGGAATGGGGGGTGGCCGTGCTGCTCGGAACAGACCAATGC---

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|58608089|gb|CK036122.1|CK036122
EST:     ATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGA                         GATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGT
genomic: ATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGAgtgagtgttc ... gaatctgcagGATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGT
EST: gi|58656403|gb|CK045083.1|CK045083
EST:     ATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGA                         GATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGT
genomic: ATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGAgtgagtgttc ... gaatctgcagGATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGT
EST: gi|58689087|gb|CK077774.1|CK077774
EST:     ATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGA                         GATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGT
genomic: ATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGAgtgagtgttc ... gaatctgcagGATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGT
EST: gi|58673732|gb|CK062418.1|CK062418
EST:     ATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGA                         GATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGT
genomic: ATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGAgtgagtgttc ... gaatctgcagGATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGT
EST: gi|58660788|gb|CK049468.1|CK049468
EST:     ATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGA                         GATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGT
genomic: ATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGAgtgagtgttc ... gaatctgcagGATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGT
EST: gi|58676612|gb|CK065299.1|CK065299
EST:     ATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGA                         GATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGT
genomic: ATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGAgtgagtgttc ... gaatctgcagGATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatcagcatgacctttatatgatattgattgtatgaaatttgtgaatctgcagGATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGTGGAATGGGGGGAATGGGAGGCCGTGCTGCTCGGAACAGACCAATGCAGG
                        tattgat  putative branch site (score: 3)
 tttatatgatattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgttcctagaatgttgtccaattctgaagtatgatcagcatgacctttatatgatattgattgtatgaaatttgtgaatctgcagGATTACTCAAACCCATTCGATCTCTTTGAATCATTATTCGAAGGCTTTGGTGGAATGGGGGGAATGGGAGGCCGTGCTGCTCGGAACAGACCAATGCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT