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

gtttgtttcatctgaacatttcttgacatgtatacagaatttcttatcccctgaatcccttcagataacttagatacacaggtcaaaattcagaagacacttactttttatttgttagagaacatatatcattggttgtcattttacagGCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCACACGAGAAACTCTGGCTATGTTTTGCCCGACACACAGGCTATGGTGGCTACGGTA

Basic information

species Oryza sativa
transcript LOC_Os01g71420.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g71420.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G34830.1 (Glycine max), 3'ss of exon 4
gtttgtttcatctgaacatttcttgacatgtatacagaatttcttatcccctgaatcccttcagataacttagatacacaggtcaaaattcagaagacacttactttttatttgttagagaacatatatcattggttgtcattttacagGCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCACACGAGAAACTCTGGCTATGTTTTGCCCGACACACAGGCTATGGTGGCTACGGTA
| ||||| ||||| | | ||| ||| ||| | || || || | || ||| | || || ||| | || || || ||||||||||| ||||| |||||||| || |||| ||||||||||| |||||||||| ||| |||| | ||| | ||||| || ||||||||||| ||
-----------------------------------aaaattt---gaattttgaatgtaatggatttgctttgatggacaattgggcatgcaagtgagattttttttctttt--------aatctattttctt--ttcacaacc-gcagGCAATTTTTGTTGGACACAACCATGGATTGGACTGGTGCTGCCCTTACGAGAAACTATGGTTATGCTATGCTAGGCACACTGGTTATGGTGGCTATGGAG

upper sequence: LOC_Os01g71420.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv08s0007g05950.t01 (Vitis vinifera), 3'ss of exon 4
gtttgtttcatctgaacatttcttgacatgtatacagaatttcttatcccctgaatcccttcagataacttagatacacaggtcaaaattcagaagacacttactttttatttgttagagaacatatatcattggttgtcattttacagGCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCACACGAGAAACTCTGGCTATGTTTTGCCCGACACACAGGCTATGGTGGCTACGGTA
| || | | | || | ||| | || ||| | | ||| | | | | | | ||| || || ||| | || | ||||| | || || || ||||| || || |||| ||||||||||| ||||||| || |||||||| ||||| |||||||||| ||||||||||| || |
----------------------------------------atgttctaggttagagcc--tgagaatagttggattttctg----aaagctgaactattgatgcaaatggggtcttactga-tattcatccct--ctgcatggtggcagGCTGTGTTTGTAGGCCACAATCATGGATTGGACTGGTGCTGCCCCTACGAGAAGCTATGGCTATGCTTTGCTAGACACACAGGTTATGGTGGCTATGGAA

upper sequence: LOC_Os01g71420.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv08s0007g05970.t01 (Vitis vinifera), 3'ss of exon 4
gtttgtttcatctgaacatttcttgacatgtatacagaatttcttatcccctgaatcccttcagataacttagatacacaggtcaaaattcagaagacacttactttttatttgttagagaacatatatcattggttgtcatttta----cagGCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCACACGAGAAACTCTGGCTATGTTTTGCCCGACACACAGGCTATGGTGGCTACGGTA
|| || | | | || ||||| ||| | ||| | | || || | || | | || || | || | | ||||| | || || || ||||| || || |||| |||||||||||| | ||||| || |||||||| |||||| | |||||||||||||| || || || |
-----------------------------------------------tagttggatttttcga---agct--gatactcagat-gaaactatggctttgctcgattgatgcaagtggggtcttactaatatttattcctcttcctggtggcagGCTGTGTTTGTAGGCCACAATCATGGATTGGACTGGTGCTGCCCATATGAGAAGCTATGGCTATGCTTTGCCAGGCACACAGGCTATGGAGGTTATGGAA

upper sequence: LOC_Os01g71420.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ10797 (Selaginella moellendorffii), 3'ss of exon 4
gtttgtttcatctgaacatttcttgacatgtatacagaatttcttatcccctgaatcccttcagataacttagatacacaggtcaaaattcagaagacacttactttttatttgttagagaacatatatcattggttgtcattttacagGCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCAC-----ACGAGAAACTCTGGCTATGTTTTGCCCGACACACAGGCTATGGTGGCTACGGTA
| || | | || | | | |||| | | | | | || || | | || ||||||| | | || || || ||||||||||||||||||||||||||| | |||||||| |||||||| || |||| |||||||| |||||
-----------------------------------------------------------------------------gtaagtgatcactcgctacaaa---acttctcgatcgactctaa---cagttctatgaatcttatcacacagGCAGTGGTGGTCGGGCATAACCACGGCCTGGATTGGTGCTGCCCAGCGGCAGTGGCGGCCTCTGGCTGTGTTTTGCTCGGCACAGTGGCTATGGAGGCTA-----

upper sequence: LOC_Os01g71420.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ26143 (Selaginella moellendorffii), 3'ss of exon 4
gtttgtttcatctgaacatttcttgacatgtatacagaatttcttatcccctgaatcccttcagataacttagatacacaggtcaaaattcagaagacacttactttttatttgttagagaacatatatcattggttgtcattttacagGCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCACACGAGAAA------CTCTGGCTATGTTTTGCCCGACACACAGGCTATGGTGGCTACGGTA
| || | | || | | | |||| | | | | | | || || | | || ||||||| | | || || || ||||||||||||||||||||||||||| || | |||||||| |||||||| || |||| |||||||| ||||
-----------------------------------------------------------------------------gtaagtgatcactcgctacaaa---acttctcgatcgattctaa---cagttctatgaatcttatcacacagGCAGTGGTGGTCGGGCATAACCACGGCCTGGATTGGTGCTGCCCAAGCGGCAGTGGCGGCCTCTGGCTGTGTTTTGCTCGGCACAGTGGCTATGGAGGCT------

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|86497190|gb|CI139823.1|CI139823
EST:     AAGCTGAATGGGGTATGATGGATGCCCTTGTCAAGAGGGCTTCAGTGAAG                         GCAATTTTCGTTGGTCACAACCACGG-CTGGATTGGTGCTGCCCACACGAG
genomic: AAGCTGAATGGGGTATGATGGATGCCCTTGTCAAGAGGGCTTCAGTGAAGgtttgtttca ... cattttacagGCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCACACGAG
EST: gi|86494914|gb|CI137547.1|CI137547
EST:     AAGCTGAATGGGGTATGATGGATGCCCTTGTCAAGAGGGCTTCAGTGAAG                         GCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCACACGAG
genomic: AAGCTGAATGGGGTATGATGGATGCCCTTGTCAAGAGGGCTTCAGTGAAGgtttgtttca ... cattttacagGCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCACACGAG
EST: gi|58599382|gb|CK009910.1|CK009910
EST:     AAGCTGAATGGGGTATGATGGATGCCCTTGTCAAGAGGGCTTCAGTGAAG                         GCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCACACGAG
genomic: AAGCTGAATGGGGTATGATGGATGCCCTTGTCAAGAGGGCTTCAGTGAAGgtttgtttca ... cattttacagGCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCACACGAG
EST: gi|88994031|gb|CI114321.1|CI114321
EST:     AAGCTGAATGGGGTATGATGGATGCCCTTGTCAAGAGGGCTTCAGTGAAG                         GCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCACACGAG
genomic: AAGCTGAATGGGGTATGATGGATGCCCTTGTCAAGAGGGCTTCAGTGAAGgtttgtttca ... cattttacagGCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCACACGAG
EST: gi|15851504|gb|BI799780.1|BI799780
EST:     AAGCTGAATGGGGTATGATGGATGCCCTTGTCAAGAGGGCTTCAGTGAAG                         GCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCACACGAG
genomic: AAGCTGAATGGGGTATGATGGATGCCCTTGTCAAGAGGGCTTCAGTGAAGgtttgtttca ... cattttacagGCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCACACGAG
EST: gi|86603554|gb|CI112314.1|CI112314
EST:     TGCCCTTGTCAAGAGGGCTTCAGTGAAG                         GCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCACACGAG
genomic: TGCCCTTGTCAAGAGGGCTTCAGTGAAGgtttgtttca ... cattttacagGCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCACACGAG
EST: gi|88462922|gb|CI519834.1|CI519834
EST:     AANCTGAATGGGGTATGATGGATGCCCTTGTCAAGAGGGCTTCAGTGAAG                         GCAATTTTCGTTGGTCACAACCACGGCCTG-AGTTGGTGCTGCCCACACGA
genomic: AAGCTGAATGGGGTATGATGGATGCCCTTGTCAAGAGGGCTTCAGTGAAGgtttgtttca ... cattttacagGCAATTTTCGTTGGTCACAACCACGGCCTGGA-TTGGTGCTGCCCACACGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacacttactttttatttgttagagaacatatatcattggttgtcattttacagGCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCACACGAGAAACTCTGGCTATGTTTTGCCCGACACACAGGCTATGGTGGCTACGGTA
   cacttac  putative branch site (score: 2)
 tcatttt  putative PPT
 ttactttttatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttcatctgaacatttcttgacatgtatacagaatttcttatcccctgaatcccttcagataacttagatacacaggtcaaaattcagaagacacttactttttatttgttagagaacatatatcattggttgtcattttacagGCAATTTTCGTTGGTCACAACCACGGCCTGGATTGGTGCTGCCCACACGAGAAACTCTGGCTATGTTTTGCCCGACACACAGGCTATGGTGGCTACGGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG