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

gtattattgttgttggaaaggctcgtgtctcttaagtttcttgcataatgcttctagtctatgcagcagccttcagacgctaacattgacactaacagtttgtaacatgactccttttatctttgtgttgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATGGCGCACTTTGATTGGACCAACTGATGCAAAAAAGGCCAAAACCTCTCAT

Basic information

species Zea mays
transcript GRMZM2G060464_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060464_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g35700.2 (Oryza sativa), 3'ss of exon 2
gtattattgttgttggaaaggctcgtgtctcttaagtttcttgcataatgcttctagtctatgcagcagccttcagacgctaacattgacact-aacagtttgtaacatgactccttttatctttgtgttgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATGGCGCACTTTGATTGGACCAACTGATGCAAAAAAGGCCAAAACCTCTCAT
                      || |   ||||   ||| ||  |||  | ||  | ||  |        | | |   ||   || ||| ||| |||||||| | |||||  |         ||| ||||| ||||||||||||||||||| | |||| |||||||||| || || ||| |  | || |||||   ||||||||| ||||||||||||| |||||| ||||  ||| ||
----------------------tcattcttcttt--tttttttaatatggattggactccttt-----atcctgatctgcct-caatgatactgaacagttt-tgacatgcttg--------tttatgttgttctttagTGGTCCAGTTCTCGTTATGATTCTGGAAAGGCCCGATGCCATCTCACACTGGCGAGTTTTGATTGGGCCAACTGATGCAAGAAAGGCTAAAATTTCTAAT
















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|211375641|gb|FL110759.1|FL110759
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|211375642|gb|FL110760.1|FL110760
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|211477829|gb|FL110766.1|FL110766
EST:     GAS-ATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|50330122|gb|CO525248.1|CO525248
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|211477830|gb|FL110767.1|FL110767
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|211477826|gb|FL110763.1|FL110763
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCTAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTG
EST: gi|211375638|gb|FL110756.1|FL110756
EST:     GAS-ATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|211477831|gb|FL110768.1|FL110768
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTAACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|211477827|gb|FL110764.1|FL110764
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGAMCTAACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|211375643|gb|FL110761.1|FL110761
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|211375634|gb|FL110752.1|FL110752
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|211375639|gb|FL110757.1|FL110757
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|211375635|gb|FL110753.1|FL110753
EST:     GAS-ATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|60351869|gb|DN218842.1|DN218842
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 59

AAGAAACCGAGGTCCAGCTTGATGCTGAGAGGGCATCTGTCTTCTATGCGGAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATGGCGCACTTTGATTGGACCAACTGATGCAAAAAAGGCCAAAACCTCTCAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 35

AAGAAACCGAGGTCCAGCTTGATGCTGAGAGGGCATCTGTCTTCTATGCGGAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATGGCGCACTTTGATTGGACCAACTGATGCAAAAAAGGCCAAAACCTCTCAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 30

AAGAAACCGAGGTCCAGCTTGATGCTGAGAGGGCATCTGTCTTCTATGCGGAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATGGCGCACTTTGATTGGACCAACTGATGCAAAAAAGGCCAAAACCTCTCAT


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 19

AAGAAACCGAGGTCCAGCTTGATGCTGAGAGGGCATCTGTCTTCTATGCGGAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATGGCGCACTTTGATTGGACCAACTGATGCAAAAAAGGCCAAAACCTCTCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgacactaacagtttgtaacatgactccttttatctttgtgttgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATGGCGCACTTTGATTGGACCAACTGATGCAAAAAAGGCCAAAACCTCTCAT
                                                tcttt  CT-rich tract
                               ttttatcttt  TA-rich tract