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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcgtgctatgtcatggtcaagttagatcattaagtttaaataacagtaacaattaacaaagtttctatctttgttgtgcagTTGATGTCTTCGCCGATGCTTCTCCGATGGTTGTTTCAGTCCTAGACGGCTACAATGTTTGTATTTTTGCCTACGGACAAACAGGAACAGGAAAGACGTT

Basic information

species Arabidopsis thaliana
transcript AT2G22610.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G22610.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os03g02290.2 (Oryza sativa), 3'ss of exon 1
----------------------------------------------------------------------------------gtagcgtgctatgtcatggtcaagttagatcattaagtttaaataaca--gtaacaattaacaaagtttctatctttgttgtgcagTTGATGTCTTCGCCGATGCTTCTCCGATGGTTGTTTCAGTCCTAGACGGCTACAATGTTTGTATTTTTGCCTACGGACAAACAGGAACAGGAAAGACGTT
                                                                                   | |   ||| | | |||  || | ||| | |||||    |     ||   |||||  |||         |  |  |  ||||||| |||||| |  |||||||| |||||  |||||  ||| ||| | || ||||||||||| || || ||||| |||||||||||||||||||| ||||| ||
gtatttctaactatgctggagtttctattgggcctctttgtcctttacagttcttgtgtttttttagacatgaaagatcaaaatggta-gctctataatgtgca-gctag-taattaaagcaatggtgcattataacatctaatctgtaaatttccaataatgtgcagCTGATGTGTATGCCGATGCATCTCCACTGGTTACTTCGGTCTTGGATGGCTACAATGTGTGCATATTTGCGTACGGACAAACAGGAACAGGGAAGACTTT

upper sequence: AT2G22610.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G092232_T01 (Zea mays), 3'ss of exon 7
------------------gtagcgtgctatgtcatggtcaagttagatcattaagtttaaataacagtaacaattaacaaagtttctatctttgttgtgcagTTGATGTCTTCGCCGATGCTTCTCCGATGGTTGTTTCAGTCCTAGACGGCTACAATGTTTGTATTTTTGCCTACGGACAAACAGGAACAGGAAAGACGTT
                    || ||||||    ||  |    | | |  | | |  ||| || ||        |  |  | |   ||    ||  ||  ||| |  ||| |  |||||||| |||||  | ||    || ||| |||| ||||||||||| || || ||||| |||||||| || |||||||||||||| ||
tgttttttttctaaaaagcaagagtgctaatctattat--gttcaaacaacttaccttatatgacttctgttgtctaatatgcaacttgaattaatgaacagATATTGTGTATGCCGATGCGTCTCCACTAGTCACATCTGTCTTAGATGGCTACAATGTATGCATCTTTGCTTACGGACAGACGGGAACAGGAAAGACTTT

upper sequence: AT2G22610.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G33340.1 (Glycine max), 3'ss of exon 7
------------------------gtagcgtgct-atgtcatggtcaagttagatcattaagtttaa-ataacagtaacaatt---aacaaagtttctatctttgttgtg-cagTTGATGTCTTCGCCGATGCTTCTCCGATGGTTGTTTCAGTCCTAGACGGCTACAATGTTTGTATTTTTGCCTACGGACAAACAGGAACAGGAAAGACGTT
                           |  ||||   | | ||       | | || |    ||||| ||||  | |||  ||   |||||   | || ||| |||| |  |||||||||| || || ||||| ||  | |||||  | || || || || |||||||||||||| || ||||| || ||||||||||||||||| ||||| ||
gtatctgaaaagtgtaacacaataactgtttgcttgagccttgaatgtcatcgctcttattatttaacataattgcaacttttctaaacaacagtgctttctatgttttaacagTTGATGTTTTTGCTGATGCATCATCAATGGTAATCTCTGTACTGGATGGCTACAATGTTTGCATCTTTGCTTATGGACAAACAGGAACAGGGAAGACATT

upper sequence: AT2G22610.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA01G02620.1 (Glycine max), 3'ss of exon 10
--------------------------------------------gtagcgt-gctatgtcatggtcaa-gttagatcattaagtttaa--ataacagtaacaatt---aacaaagtttctatctttgttgtg-cagTTGATGTCTTCGCCGATGCTTCTCCGATGGTTGTTTCAGTCCTAGACGGCTACAATGTTTGTATTTTTGCCTACGGACAAACAGGAACAGGAAAGACGTT
                                             |  | | ||| |   ||  | |     ||||  |||   || |  ||||  | |||  ||   |||||   |  | ||| |||| |  |||||||||| || || ||||| ||  | |||||  | || || || || |||||||||||||| || ||||| || || |||||||||||||| ||||| ||
gtatctgaaaagtgtaacacaatagctatttgcttgagccttgaatgtcatcgctcttatatatttagtacaagatttttattatttatcataattggaacttttctaaacaacagtgttttctatgttttaacagTTGATGTTTTTGCTGATGCATCATCAATGGTAATCTCTGTACTGGATGGCTACAATGTTTGCATCTTTGCTTATGGGCAAACAGGAACAGGGAAGACATT

upper sequence: AT2G22610.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv18s0001g07800.t01 (Vitis vinifera), 3'ss of exon 7
---gtagcgtgctatgtca-tggtcaagttagatcattaagt-ttaaataacagta-acaatt------aacaaagtttctatctttgttgtg----cagTTGATGTCTTCGCCGATGCTTCTCCGATGGTTGTTTCAGTCCTAGACGGCTACAATGTTTGTATTTTTGCCTACGGACAAACAGGAACAGGAAAGACGTT
   |  |  |    | ||| | ||   | ||  | | | | | ||  || | | |  | | ||      |  || | |  | ||| | |||||    |||||||  |||  || ||||| || || |||||  |||| || ||||| ||||||||||| ||||| ||||| || || |||||||| |||||||| || ||
attgctgaatttgttctcactagttgtgataatttactcactatttcatgatattgcatagtttgtaggactaatgctgatgtctcttttgtgataacagTTGACATCTCTGCGGATGCCTCACCTATGGTAATTTCGGTGCTAGATGGCTACAATGTCTGTATATTTGCATATGGGCAAACAGGGACAGGAAAAACCTT

upper sequence: AT2G22610.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv00s0218g00050.t01 (Vitis vinifera), 3'ss of exon 9
--------gtagcg-tgctatgtcatggtca-agttagatcattaagtttaaataacagtaacaattaacaaagtttctatctttgttgtgcagTTGATGTCTTCGCCGATGCTTCTCCGATGGTTGTTTCAGTCCTAGACGGCTACAATGTTTGTATTTTTGCCTACGGACAAACAGGAACAGGAAAGACGTT
         ||    | |||  |  ||| || |||      |||     |   | |   |  || | |   |   || |  |||   |   |||||||||| || || ||||| || || |||||  |||||||  |||| || |||||||| ||||| ||||| || || |||||||| ||||||||||| ||
gtgtgcatatattactactaattggtggacacagtcttgctattttaactttgtgaactttgcattaagtgagaatttt--cttgtcttaacagTTGATGTGTTTGCGGATGCGTCACCAATGGTGATTTCAGTGTTAGATGGATACAATGTCTGTATATTTGCATATGGGCAAACAGGCACAGGAAAGACATT

upper sequence: AT2G22610.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ04247 (Selaginella moellendorffii), 3'ss of exon 8
gtagcgtgctatgtcatggtcaagttagatcattaagtttaaataacagtaacaattaacaaa---gtttctatctttgttgtgcagTTGATGTCTTCGCCGATGCTTCTCCGATGGTTGTTTCAGTCCTAGACGGCTACAATGTTTGTATTTTTGCCTACGGACAAACAGGAACAGGAAAGACGTT
                                 | ||| ||    | |||    ||| ||||     |     | |  ||||||||| ||| || || || ||  | |||||| | ||||| || ||||| || |||||||| || || || |||||||||||||||||||| || || || || ||
--------------------------------gtgagtatatggcaaagtctatattcacaagctgatcctcgtttccgttgtgcagCTGAAGTGTTTGCAGACACGTCTCCGGTCGTTGTATCTGTCCTGGATGGCTACAACGTGTGCATATTTGCCTACGGACAAACAGGTACTGGCAAAACATT

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|86070292|gb|DR366049.1|DR366049
EST:     CNAGAAAAGTTTCAAGTTTGACAGAGTTTATACACCGAAAGATGGTCAAG                         TTGATGTCTTCGCCGATGCTACTCCGATGGTTGTTTCAGTCCTAGACGGCT
genomic: CAAGAAAAGTTTCAAGTTTGACAGAGTTTATACACCGAAAGATGGTCAAGgtagcgtgct ... tgttgtgcagTTGATGTCTTCGCCGATGCTTCTCCGATGGTTGTTTCAGTCCTAGACGGCT
EST: gi|86070293|gb|DR366050.1|DR366050
EST:     CAAGAAAAGTTTCAAGTTTGACAGAGTTTATACNCCGAANGATGGTCAAG                         TTGATGTCTTCGCCGATGCTTCTCCGATGGTTGTTTCAGTCCTAGACGGCT
genomic: CAAGAAAAGTTTCAAGTTTGACAGAGTTTATACACCGAAAGATGGTCAAGgtagcgtgct ... tgttgtgcagTTGATGTCTTCGCCGATGCTTCTCCGATGGTTGTTTCAGTCCTAGACGGCT
EST: gi|86070294|gb|DR366051.1|DR366051
EST:     CAAGAAAAGTTTCAAGTTTGACAGAGTTTATACACCGAAAGATGGTCAAG                         TTGATGTCTTCGCCGATGCTTCTCCGATGGTTGTTTCAGTCCTAGACGGCT
genomic: CAAGAAAAGTTTCAAGTTTGACAGAGTTTATACACCGAAAGATGGTCAAGgtagcgtgct ... tgttgtgcagTTGATGTCTTCGCCGATGCTTCTCCGATGGTTGTTTCAGTCCTAGACGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattaagtttaaataacagtaacaattaacaaagtttctatctttgttgtgcagTTGATGTCTTCGCCGATGCTTCTCCGATGGTTGTTTCAGTCCTAGACGGCTACAATGTTTGTATTTTTGCCTACGGACAAACAGGAACAGGAAAGACGTT
                        aattaac  putative branch site (score: 2)
                                   tttctatctttgtt  putative PPT
        tttaaataacagtaac  TA-rich tract