Sequence
atgc intronic sequence ATGC exonic sequencegtaactaatcattctgtattgctttgaattttactctgttacgagctggtatcttttctttgttattttagtggttgttgatttgaatatcttgtgtacacagTGGTGGCTACAACATTAAGACTGGACCTGGCTGCTCAATTGAGCTCATGAAATTCGACATGGGCGGTTCAGCTGCTGTTCTTGGCGCTGCGAAAGCTATT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G24200.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g55140.1 (Oryza sativa), 3'ss of exon 4
---------gtaactaatcattctgt-----attgctttga---attttactctgttacg---agctggtatcttttctttgttattttagtggttgttg-atttgaatatct--tgtgtacacagTGGTGGCTACAACATTAAGACTGGACCTGGCTGCTCAATTGAGCTCATGAAATTCGACATGGGCGGTTCAGCTGCTGTTCTTGGCGCTGCGAAAGCTATT
| | ||| ||| ||||| | | | | | | ||| || | || ||||||| | || || ||||| || | |||| || | | | | |||||||||||||||||||||||||||||| |||||| |||||||| ||||| || |||||||| || || || || ||| |||| || || |||||| |
gtttgtgaaacatatgcatattttgtgaactattgcagtaacatacatcattgtgtaacataaatatgccatcttttatatggataattgttggttcttacaattgattaaccgatttttttgcagTGGTGGCTACAACATTAAGACTGGACCAGGCTGCAGTATTGAGCTGATGAAGTTTGACATGGGAGGCTCTGCAGCAGTTTTTGGTGCAGCAAAAGCTTTG
upper sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G028114_T01 (Zea mays), 3'ss of exon 8
----gtaactaatcattctgtattgctttgaattttactctgttacgagctggtatcttttctttgttattt--tagtggttgttgatttgaatatcttgtgtacacagTGGTGGCTACAACATTAAGACTGGACCTGGCTGCTCAATTGAGCTCATGAAATTCGACATGGGCGGTTCAGCTGCTGTTCTTGGCGCTGCGAAAGCTATT
||| || | |||| | | || | |||| || | | | ||| || | | | || ||| | || | |||||||||||||||||||||||| || || |||||| || ||||| |||||||| |||||||| || || || ||| | |||| || || |||| | |
gtttgtag-tacttgccacatatttagtgggtttatgaaaagttagaagtagacaagtagatggaaccgtttgttatttttcttatgcttcaattgccaatgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAACATCGAGCTGATGAAATTTGACATGGGAGGCTCTGCAGCTATATTTGGTGCAGCTAAAGATTTG
upper sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G178958_T01 (Zea mays), 3'ss of exon 4
----gtaactaatcattctgtattgctttgaattttactctgttacgagctggtatctt-------ttctttgttattttagtggttgttgatttgaatatcttgtgtacacagTGGTGGCTACAACATTAAGACTGGACCTGGCTGCTCAATTGAGCTCATGAAATTCGACATGGGCGGTTCAGCTGCTGTTCTTGGCGCTGCGAAAGCTATT
||| || | |||| | | || | |||| || | | | ||||||||||| | | ||| |||| | || | |||||||||||||||||||||||| || || |||||| || ||||| |||||||| |||||||| || || || ||||| |||| || || |||||| |
gtttgtag-tacttgccacatatttagtgggtttatgaaaagttagaagtagacaagtagatggaaccgtttgttatttttcttatgcttggtttg-----ccaatgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAAATTTGACATGGGAGGCTCTGCAGCTGTATTTGGTGCAGCTAAAGCTTTG
upper sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G126913_T01 (Zea mays), 3'ss of exon 4
----------gtaactaatcattctgtattgctttgaattttactctgttacgagctggtatcttttctttgttattttagtggttgttgatttgaatatcttgtgtacacagTGGTGGCTACAACATTAAGACTGGACCTGGCTGCTCAATTGAGCTCATGAAATTCGACATGGGCGGTTCAGCTGCTGTTCTTGGCGCTGCGAAAGCTATT
| | | ||| || | | || ||| || || | | ||||||||||| | | |||||||| | || | |||||||||||||||||||||||| || || |||||| || ||||| |||||||| |||||||| || || || ||||| |||| || || |||||| |
gtttgtagtacttgccacatatttagtgggtttataaaagttagaagtagacaagtagatggaaccg-tttgttatttttcttatgcttgatttg-----ccaatgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAAATTTGACATGGGAGGCTCTGCAGCTGTATTTGGTGCAGCTAAAGCTTTG
upper sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G018558_T01 (Zea mays), 3'ss of exon 4
----gtaactaatcattctgtattgctttgaatttt---actctgttacgagctggtatctt---ttctttgttattttagtggttgttgatttgaatatcttgtgtacacagTGGTGGCTACAACATTAAGACTGGACCTGGCTGCTCAATTGAGCTCATGAAATTCGACATGGGCGGTTCAGCTGCTGTTCTTGGCGCTGCGAAAGCTATT
||| || | |||| || | || | | | | | ||| | ||||||||||| | | |||||||| | || | |||||||||||||||||||||||| || || |||| | || ||||| |||||||| |||||||| || || | ||||| |||| || || |||||| |
gtttgtag-tacttgccacatatttattgggtttataaaagttagaagtagacaagtagatggaaccgtttgttatttttcttatgcttgatttg-----ccaatgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTACAGCATCGAGCTGATGAAATTTGACATGGGAGGCTCTACAGCTGTATTTGGTGCAGCTAAAGCTTTG
upper sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G388453_T01 (Zea mays), 3'ss of exon 7
----------gtaactaatcattctgtattgctttgaattttactctgttacgagctggtatcttttctttgttattttagtggttgttgatttgaatatcttgtgtacacagTGGTGGCTACAACATTAAGACTGGACCTGGCTGCTCAATTGAGCTCATGAAATTCGACATGGGCGGTTCAGCTGCTGTTCTTGGCGCTGCGAAAGCTATT
| | | ||| || | | || ||| || || | | ||||||||||| | | |||||||| | || | |||||||||||||||||||||||| || || |||| | || ||||| |||||||| |||||||| || || || ||||| |||| || || |||||| |
gtttgtagtacttgccacatatttagtgggtttataaaagttagaagtagacaagtagatggaaccg-tttgttatttttcttatgcttgatttg-----ccaatgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTACAGCATCGAGCTAATGAAATTTGACATGGGAGGCTCTGCAGCTGTATTTGGTGCAGCTAAAGCTTTG
upper sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 4
gtaactaatcattctgtattgctttgaattttactctgttacgagctggtatcttttctttgttattttagtggttgttgatttgaatatcttgtgtacacagTGGTGGCTACAACATTAAGACTGGACCTGGCTGCTCAATTGAGCTCATGAAATTCGACATGGGCGGTTCAGCTGCTGTTCTTGGCGCTGCGAAAGCTATT
| | | | || | | | | || | | | ||| | || || | | | || | ||| | | || | || | | ||||||||||||||||| ||||||||||||||||| |||||||||||||||||||| || ||||| |||||||| || ||| | || | || |||||| |
-ttattttttcttattcaatataataaaatattcatcattataa--tgataacatctattaatctctttgatttattttcttatgttgtctacatattattagTGGTGGCTACAACATCAAGACTGGACCTGGCTGTTCAATTGAGCTCATGAAATTTGATATGGGTGGTTCAGCAGCAGTTTTAGGAACAGCAAAAGCTCTC
upper sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G08150.1 (Glycine max), 3'ss of exon 4
gtaactaatcattctgtattgctttgaattttactctgttacgagctggtatcttttctttgttattttagtggttgttgatttgaatatcttgtgtac--acagTGGTGGCTACAACATTAAGACTGGACCTGGCTGCTCAATTGAGCTCATGAAATTCGACATGGGCGGTTCAGCTGCTGTTCTTGGCGCTGCGAAAGCTATT
||| | || || | || | | || | | | ||| | || | | | | ||| | |||| || || ||| | || || ||||||||||||||||| ||||||||||||||||| |||||||| ||||||||||| || ||||| |||||||| || ||| | || | ||||||||| ||
-taattgattcttatttaatataataaaatatccatcattataa--tgaaaacgtctatttatctctttaa--attattattttatgttgtctgcatattattagTGGTGGCTACAACATCAAGACTGGACCTGGCTGTTCAATTGAACTCATGAAATTTGATATGGGTGGTTCAGCAGCAGTTTTAGGAACAGCGAAAGCTCTT
upper sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G19350.1 (Glycine max), 3'ss of exon 4
gtaactaatcattctgtattgctttgaattttactctgttacgagctggtatcttttctttgttattttagtggttgttgatttgaatatcttgtgtac--acagTGGTGGCTACAACATTAAGACTGGACCTGGCTGCTCAATTGAGCTCATGAAATTCGACATGGGCGGTTCAGCTGCTGTTCTTGGCGCTGCGAAAGCTATT
||| | || || | || | | || | | | ||| | || | | | | ||| | |||| || || ||| | || || ||||||||||||||||| ||||||||||||||||| |||||||| ||| ||||||| || ||||| |||||| | | ||| | || | |||||||| ||
-taattgattcttatttaatataataaaatatccatcattataa--tgaaaacgtctatttatctctttaa--attattattttatgttgtctgcatattattagTGGTGGCTACAACATCAAGACTGGACCTGGCTGTTCAATTGAACTCGTGAAATTTGATATGGGTGGTTCAACAACAGTTTTAGGAACAACGAAAGCTCTT
upper sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G22730.1 (Glycine max), 3'ss of exon 4
gtaactaatcattctgtattgctttgaattttactctgttacgagctggtatcttttctttgttattttagtggttgttgatttgaatatcttgtgtacacagTGGTGGCTACAACATTAAGACTGGACCTGGCTGCTCAATTGAGCTCATGAAATTCGACATGGGCGGTTCAGCTGCTGTTCTTGGCGCTGCGAAAGCTATT
| || | ||| | | | ||| | ||| | || | | || |||| | ||| || ||| | ||| ||||||||||||||||| ||||| ||||||||||| | ||||| || |||||||| || ||||||||||| ||||| ||| |||| || || |||||| |
-ttgctggaggtgctggtt--cctcgaaaaccagagggtttgaacctaacagtaataattacaatttttctttgttcttttttttttatttgcatgttattagTGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAAATTTGATATGGGCGGTTCTGCTGCAGTTTTTGGAGCAGCAAAAGCTCTA
upper sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv11s0037g00180.t01 (Vitis vinifera), 3'ss of exon 4
gtaactaatcattctgtattgctttgaattttactctgttacgagctg-gtatcttttctttgttattttagtggttgttgatttgaatatcttgtgtacacagTGGTGGCTACAACATTAAGACTGGACCTGGCTGCTCAATTGAGCTCATGAAATTCGACATGGGCGGTTCAGCTGCTGTTCTTGGCGCTGCGAAAGCTATT
| | | | || | || || ||| | || | || | | | | | | ||| | | | | || | | || ||||||||||||||||| ||||||||||||||||| || |||||||||||||| || || ||||| ||||||||||| ||||| || || || ||||| |||
----tttgttttcaaaaagtggccagtataataatctatgttattatgtgcatttgattctccatctatacgtgttcttaaacatttatctttcatggttttagTGGTGGCTACAACATCAAGACTGGACCTGGCTGTTCTATTGAGCTCATGAAGTTTGATATGGGGGGTTCAGCTGCGGTTCTCGGTGCAGCAAAAGCCATTMapped 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|164197486|gb|ES023680.1|ES023680EST: GACCAAACTTGCTCTTGTTGG-AAAGGATTGACCTTTGACAG TGGTGGCTACAACATTAAGACTGGACCTGGCT
genomic: GACCAAACTTGCTCTTGTTGGAAAAGGATTGACCTTTGACAGgtaactaatc ... gtgtacacagTGGTGGCTACAACATTAAGACTGGACCTGGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatcttttctttgttattttagtggttgttgatttgaatatcttgtgtacacagTGGTGGCTACAACATTAAGACTGGACCTGGCTGCTCAATTGAGCTCATGAAATTCGACATGGGCGGTTCAGCTGCTGTTCTTGGCGCTGCGAAAGCTATT
tgttgat putative branch site (score: 4)
ttttctttgttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactaatcattctgtattgctttgaattttactctgttacgagctggtatcttttctttgttattttagtggttgttgatttgaatatcttgtgtacacagTGGTGGCTACAACATTAAGACTGGACCTGGCTGCTCAATTGAGCTCATGAAATTCGACATGGGCGGTTCAGCTGCTGTTCTTGGCGCTGCGAAAGCTATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT