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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAGGTTTCAAGGTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctgttacacttacacacttttttaaaacttcagctcttttttttttaaagaaaaatgctgttctgctatgcttgcaattgctcaattttttttttgtatggtgaag

Basic information

species Oryza sativa
transcript LOC_Os01g01307.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01307.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G376727_T01 (Zea mays), 5'ss of exon 3
TGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAGGTTTCAAGGTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctgttacacttacacacttttttaaaacttcagctcttttttttttaaagaaaaatgctgttctgctatgcttgcaattgctcaattttttttttgtatggtgaag
|||| | ||  ||| |||| |||||||||||  |||||||||||| || |||||||| ||  ||||||| || ||||||||||||||| |||| ||||||||     |     | |   |  || | |   | || | |  | |  | ||| | | |  | |   | || |  ||| ||   | ||  |  ||   | ||             
TGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccccccccccccccgacctctactatacat-aattttagtgtttcttatgttataca-tcttgtattatcctcttattttttacatcgctattgc-----------

upper sequence: LOC_Os01g01307.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G376727_T02 (Zea mays), 5'ss of exon 3
TGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAGGTTTCAAGGTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctgttacacttacacacttttttaa-----aacttcagctcttttttttttaaagaaaa-atgctgttctgctatgcttgcaattgct--caattttttttttgtat--ggtgaag---------------------------
|||| | ||  ||| |||| |||||||||||  |||||||||||| || |||||||| ||  ||||||| || ||||||||||||||| |||| ||||||||     |     | |   |  || | |   |     || || ||   || || | ||| | |     |  | | ||  |||  ||   || |||     ||      | ||||   || ||                            
TGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccccccccccccccgacctctactatacataattttagtgtttcttatgttatacatcttgtattatcctcttattttttacatcgctattgcttggcccatggtatttagttaaatctaatgttttgtatctgttcaaggag

upper sequence: LOC_Os01g01307.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G376727_T05 (Zea mays), 5'ss of exon 3
TGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAGGTTTCAAGGTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctgttacacttacacacttttttaa-----aacttcagctcttttttttttaaagaaaa-atgctgttctgctatgcttgcaattgct--caattttttttttgtat--ggtgaag------------------------
|||| | ||  ||| |||| |||||||||||  |||||||||||| || |||||||| ||  ||||||| || ||||||||||||||| |||| ||||||||     |     | |   |  || | |   |     || || ||   || || | ||| | |     |  | | ||  |||  ||   || |||     ||      | ||||   || ||                         
TGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccccccccccccccgacctctactatacataattttagtgtttcttatgttatacatcttgtattatcctcttattttttacatcgctattgcttggcccatggtatttagttaaatctaatgttttgtatctgttcaag

upper sequence: LOC_Os01g01307.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G067476_T01 (Zea mays), 5'ss of exon 3
TGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAGGTTTCAAGGTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctgttacacttacacacttttttaaaacttcagctctttttttt-ttaaagaaaaatgctgttctgctatgcttgcaattgctcaattttttttttgtatggtgaag
|||||| ||  ||| |||| |||||||||||  |||||||||||| || |||||||| ||  | ||||| || ||||||||||||||| | || ||||||||     |     |||||   | ||  | | |||  ||  |   |  |    ||||     | |  |  ||     || ||   |    |||   ||  |              
TGCTTCACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATCATTACATACCGTGTTCCCACAAAGACAGCTCTTCAGgtcccccccaccccactttatctctactgttaaatgtcttcaagtcgtccaattaatcgcgattagtcgtccaagttggtttggaccaatcacgattaat--------------

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|88249475|gb|CI249324.1|CI249324
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|88908088|gb|CI090684.1|CI090684
EST:     GTTCACCTGCGGTTATNACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|88976399|gb|CI024616.1|CI024616
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|5004937|gb|AU070175.1|AU070175
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|86506952|gb|CI149585.1|CI149585
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|88975507|gb|CI021589.1|CI021589
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|55431192|gb|CV728603.1|CV728603
EST:     GGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|55441563|gb|CV734105.1|CV734105
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|87010511|gb|CI283586.1|CI283586
EST:     CAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: CAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|86532074|gb|CI172280.1|CI172280
EST:     AGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTACACTTGATGTTCTTGCTGAGAGGCCT
genomic: AGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|86530842|gb|CI171048.1|CI171048
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|88907999|gb|CI090595.1|CI090595
EST:     CACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: CACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|15852886|gb|BI805682.1|BI805682
EST:     GTTCACCT-CGGTTA-TACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GA-GCCTATTCAACCCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCC
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAA-CCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCC
EST: gi|86415683|gb|CI029694.1|CI029694
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|87027081|gb|CI261528.1|CI261528
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAGCCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|55431655|gb|CV728843.1|CV728843
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|33660042|gb|CF291009.1|CF291009
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCC
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAA-CCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCC
EST: gi|88228632|gb|CI228112.1|CI228112
EST:     ACCTGCGATTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: ACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|86415979|gb|CI029990.1|CI029990
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|87032410|gb|CI264191.1|CI264191
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|88837885|gb|CI371463.1|CI371463
EST:     CACAAA-GCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGA-GCCT
genomic: CACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|427829|gb|D23969.1|D23969
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|86413465|gb|CI067870.1|CI067870
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|86416814|gb|CI030825.1|CI030825
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT