Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtctttggtcaacatcagattcatccccagtgttttggcttgccattaatttttccattgtgagctctgtttatcaatctgacctgcctttttgctccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATATGTGGTCTGTGGGCTGCATAATGGCAGAGCTTTTGGCCAAAGAACCATTA

Basic information

species Oryza sativa
transcript LOC_Os04g41100.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41100.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G139038_T01 (Zea mays), 3'ss of exon 2
gtaggtctttggtcaacatcagattcatccccagtgttttggcttgccattaa--tttttccattgtgagctctgttta-tcaatct--gacctgccttt-ttgctccttct-----cagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATATGTGGTCTGTGGGCTGCATAATGGCAGAGCTTTTGGCCAAAGAACCATTA
||||||| | || ||||||||||||| ||  ||||||||||| || |   |||  || |||  ||| ||| |||||||  |||| |   |||   ||||| ||||||||| |     |||||| |||||||| || |||||||| ||||| |||||||| || |||||||||||||| |||||||| |||||||| |||||  | |||||||||||||||
gtaggtcatcggacaacatcagattcctcagcagtgttttggttttcttctaaagttattcagttgagagttctgtttggtcaaccaaggactcacctttcttgctccttgtggctacagGGCCCCAGAACTGTTGTTAGGAACAAAGGAGTATTCTACTGCTATTGATATGTGGTCCGTGGGCTGTATAATGGCTGAGCTCCTTGCCAAAGAACCATTA

upper sequence: LOC_Os04g41100.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G179097_T07 (Zea mays), 3'ss of exon 2
gtaggtctttggtcaacatcagattcatccccagtgttttggcttgccattaa--tttttccattgtgagctctgttta-tcaatct---gacctgccttt-ttgctccttct-----cagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATATGTGGTCTGTGGGCTGCATAATGGCAGAGCTTTTGGCCAAAGAACCATTA
                    |||| | ||  ||||||||||| || |   |||  || |||  ||| ||| |||||||  ||||      |||   | ||| ||||||||| |     |||||| |||||| | || |||||||| ||||| |||||||| || ||||||||||||||||||||||| |||||||| |||||| | ||||||||||| |||
--------------------agatcc-tcagcagtgttttggttttcttctaaagttattcagttgagagttctgtttggtcaaatcaaggactcacttttcttgctccttgtggctacagGGCCCCAGAATTGTTGTTAGGAACAAAGGAGTATTCTACTGCTATTGATATGTGGTCTGTGGGCTGTATAATGGCTGAGCTTCTTGCCAAAGAACCGTTA

upper sequence: LOC_Os04g41100.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G179097_T04 (Zea mays), 3'ss of exon 2
gtaggtctttggtcaacatcagattcatccccagtgttttggcttgccattaa--tttttccattgtgagctctgttta-tcaatct---gacctgccttt-ttgctccttct-----cagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATATGTGGTCTGTGGGCTGCATAATGGCAGAGCTTTTGGCCAAAGAACCATTA
||||||| | || ||||||||||| | ||  ||||||||||| || |   |||  || |||  ||| ||| |||||||  ||||      |||   | ||| ||||||||| |     |||||| |||||| | || |||||||| ||||| |||||||| || ||||||||||||||||||||||| |||||||| |||||| | ||||||||||| |||
gtaggtcatcggacaacatcagatcc-tcagcagtgttttggttttcttctaaagttattcagttgagagttctgtttggtcaaatcaaggactcacttttcttgctccttgtggctacagGGCCCCAGAATTGTTGTTAGGAACAAAGGAGTATTCTACTGCTATTGATATGTGGTCTGTGGGCTGTATAATGGCTGAGCTTCTTGCCAAAGAACCGTTA

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|218494622|gb|FG958132.1|FG958132
EST:     CGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAG                         GGCGCCA-AACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
genomic: CGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
EST: gi|58691737|gb|CK080424.1|CK080424
EST:     GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAG                         GGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
genomic: GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
EST: gi|29640024|gb|CB645033.1|CB645033
EST:     GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAG                         GGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
genomic: GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
EST: gi|58587583|gb|CF985891.1|CF985891
EST:     GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAG                         GGCGCCAGAACTATTA
genomic: GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTA
EST: gi|33678455|gb|CF306694.1|CF306694
EST:     GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGCGGTACAG                         GGCGCCAGAACTATTATTATGAACGAAAGAATATTCTACCGCCATTGATAT
genomic: GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
EST: gi|163929543|gb|EG709310.1|EG709310
EST:     GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAG                         GGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
genomic: GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
EST: gi|58686625|gb|CK075312.1|CK075312
EST:     GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAG                         GGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
genomic: GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
EST: gi|58687429|gb|CK076116.1|CK076116
EST:     GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAG                         GGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
genomic: GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
EST: gi|29679248|gb|CB675523.1|CB675523
EST:     GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAG                         GGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
genomic: GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttccattgtgagctctgtttatcaatctgacctgcctttttgctccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATATGTGGTCTGTGGGCTGCATAATGGCAGAGCTTTTGGCCAAAGAACCATTA
                          atctgac  putative branch site (score: 3)
                                cctgcctttttgctcc  CT-rich tract
                   tttatcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtctttggtcaacatcagattcatccccagtgttttggcttgccattaatttttccattgtgagctctgtttatcaatctgacctgcctttttgctccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATATGTGGTCTGTGGGCTGCATAATGGCAGAGCTTTTGGCCAAAGAACCATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC