Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taccagaatttaccatgcttatatgttgaacataaatacactccatcagttcgatcatggagttatttccagttaataaaagatatctgactccatggagTCATTTCCAGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGGTGGCCTTCTCTTCACCAAGGGGGGCTCAATTCTTCTCTT

Basic information

species Oryza sativa
transcript LOC_Os04g51400.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51400.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G140924_T01 (Zea mays), 3'ss of exon 2
taccagaatttaccatgcttatatgttgaacataaatacactccatcagttcgatcatgga--gttatttccagttaataaaagatatctgactccatggagTCATTTCCAGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGGTGGCCTTCTCTTCACCAAGGGGGGCTCAATTCTTCTCTT----------------
                |  |||   || || |   |||     |||  | | |  | || |  | || |    ||       | || |||||||   |     || ||| |  | ||||     |||| ||||||| || |||||||||||||| ||||| || ||||| || || |||||||| || ||||||||||||||                
----------------gggtattaattaaatactgatatcaggcat--ggtaggacctgaatcggtaatggtcgtgctcgggaaatgtctgacttgttcctaccacttctaactccagGCAGTTATCTGACATGGAGGAGCACATGGGAAGACGAACAGTCGGCGGCCTGCTATTAACCAAGGGAGGATCAATTCTTCTCTTCAGAGAGGACGGTTCG

upper sequence: LOC_Os04g51400.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G053909_T01 (Zea mays), 3'ss of exon 2
taccagaatttaccatgcttatatgttgaacataaatacactccatcagttcgatcatggagttatttccagttaataaaagatatctgactccatggagTCATTTCCAGTTTCAGGTGA--------ACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGGTGGCCTTCTCTTCACCAAGGGGGGCTCAATTCTTCTCTT--------
             | || | ||   |  | || |  ||    |  |      | ||   | | | |  || |||    | |  |  |||||  | |  |  |||||| | |||||||| |          |||| |||||||||| |||||||||||||| ||||| || ||||| |||||||||||||| || || || ||||||||        
------------gcgtg-tcatgaatccagcacat-tattacctgtttaccaggtctgagtgatttaacctgtt--cgagaagtgcctgacctcgtccaaccatttctaatttcagGTAATTATCACTGTATCTGACATGGATGAGCACATGGGAAGACGAACAGTCGGCGGCCTCCTCTTCACCAAGGGAGGATCCATCCTTCTCTTCAGAGAAG
















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|29676636|gb|CB672911.1|CB672911
EST:     CAGCCGGGTCACACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGG--A-                         --A-----AGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... ctccatggagTCATTTCCAGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
EST: gi|58689183|gb|CK077870.1|CK077870
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGG--A-                         --A-----AGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... ctccatggagTCATTTCCAGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
EST: gi|29676638|gb|CB672913.1|CB672913
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGG--A-                         --A-----AGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... ctccatggagTCATTTCCAGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
EST: gi|58594947|gb|CF993255.1|CF993255
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGG--A-                         --A-----AGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... ctccatggagTCATTTCCAGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
EST: gi|29643914|gb|CB648921.1|CB648921
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGG--A-                         --A-----AGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... ctccatggagTCATTTCCAGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
EST: gi|29643362|gb|CB648369.1|CB648369
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGG--A-                         --A-----AGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... ctccatggagTCATTTCCAGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
EST: gi|29688856|gb|CB685131.1|CB685131
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGG--A-                         --A-----AGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... ctccatggagTCATTTCCAGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
EST: gi|29671276|gb|CB667551.1|CB667551
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGG--A-                         --A-----AGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... ctccatggagTCATTTCCAGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
EST: gi|29622172|gb|CB627183.1|CB627183
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAG                         TCATTTCCAGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... ctccatggagTCATTTCCAGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
EST: gi|58692009|gb|CK080696.1|CK080696
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGG--A-                         --A-----AGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... ctccatggagTCATTTCCAGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagttcgatcatggagttatttccagttaataaaagatatctgactccatggagTCATTTCCAGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGGTGGCCTTCTCTTCACCAAGGGGGGCTCAATTCTTCTCTT
                                       atctgac  putative branch site (score: 3)
                         agttaataaaagatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taccagaatttaccatgcttatatgttgaacataaatacactccatcagttcgatcatggagttatttccagttaataaaagatatctgactccatggagTCATTTCCAGTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGGTGGCCTTCTCTTCACCAAGGGGGGCTCAATTCTTCTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
-accagaa
- - - - - - ccatgct
- - - - - - - - - - - -tgttgaa
- - - - - - - - - - - - - - - - - - - - ctccatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -catggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaa