Sequence
atgc intronic sequence ATGC exonic sequencegtatggaatcatcactcttttgccttttgattatctgaaaacatttacattatcagtcacacatataacattttgctttgagtcatatagTGAACTCTACAAAAACGAGATTCAAGGAACTATACCTTCTGAGCTTGGAAATCTGAAGAGTCTAATCAGTTTGGATCTGTACAACAACAATCTCACCGGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G43740.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G43740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G815009_T01 (Zea mays), 3'ss of exon 2
--------gtatggaatcatcactcttttgccttttgattatctgaaaacatttacattatcagtcacacatataacattttgctttg--agtcatatagTGAACTCTACAAAAACGAGATTCAAGGAACTATACCTTCTGAGCTTGGAAATCTGAAGAGTCTAATCAGTTTGGATCTGTACAACAACAATCTCACCGGG
|| | | | | ||| ||||| || ||| || | | | | ||| | ||| | | | |||| ||||| ||||| ||| ||||||||||| || |||||||||||||| ||| |||||| |||||| || ||||| ||||||| ||||| | | |||
tgatatagttaaatatttagatatttttcatagtttgacatgtgcctgtcaattattcatccaataattaaactggtattgaccattggcactgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAATTTGAAGAATCTAATAAGCTTGGACTTGTACAAGAACAACATTTCGGGG
upper sequence: AT3G43740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G121820_T01 (Zea mays), 3'ss of exon 2
------gtatggaatcatcactcttttgccttttgattatctgaaaacatttacattatcagtcacacat-ataacatttt-----gctttgagtcatatagTGAACTCTACAAAAACGAGATTCAAGGAACTATACCTTCTGAGCTTGGAAATCTGAAGAGTCTAATCAGTTTGGATCTGTACAACAACAATCTCACCGGG
|| || |||| | | |||| | || | | ||| || | | ||| || |||||| | | | | | | | | || ||||| || || || | ||||||||||| || |||||||||||||| ||| |||||| |||||| || || || ||||||| ||||| | | |||
tttgcagttatgactcatgatacaagggcctggta--tactcagacattttttcacttagtttgacaaattataacagtattgaccgttagcactgaaacagGGAACTTTATAAGAATAACATTCAAGGAACAATCCCTTCTGAGCTTGGCAATTTGAAGAATCTAATAAGCTTCGACTTGTACAAGAACAACATTTCGGGG
upper sequence: AT3G43740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G44250.2 (Glycine max), 3'ss of exon 2
--gtatggaatcatcact--cttttgccttttgattatctgaaaacat----ttacattatcagtcacacata-taacattttgctttgagtc-atatagTGAACTCTACAAAAACGAGATTCAAGGAACTATACCTTCTGAGCTTGGAAATCTGAAGAGTCTAATCAGTTTGGATCTGTACAACAACAATCTCACCGGG-
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tattactaaattggtatttgctgtggctctcttattgttgtgaactatagcatttcatacctgttagtgtttaatgaggttttctttttattggatgtagTGAGTTGTACAAAAACAACATTCAAGGAACTATTCCTCCGGAACTTGGAAACCTGAAGAGTCTAGTTAGCTTGGACTTGTACAACAACAACAT-ATCAGGC
upper sequence: AT3G43740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G04520.1 (Glycine max), 3'ss of exon 2
--------gtatggaatcatcactcttttgccttttg--attatctgaaaacatttacat-tatcagtcacacatataacattttgctttgagtcatatagTGAACTCTACAAAAACGAGATTCAAGGAACTATACCTTCTGAGCTTGGAAATCTGAAGAGTCTAATCAGTTTGGATCTGTACAACAACAATCTCACCGGG-
| ||| || || | | | | ||| | | || | | |||| | | | ||| || | || | || || |||||| | ||||||||| | |||||||||||||| ||| | || |||||||| ||||||||||| | || ||||| ||||||||||||| | | | ||
gattgatcgattggtattttctgtggctctcttattgttgtgaactatagaattttatacctgttagtgtttaatgtggttttct-tttcattggatgtagTGAGTTGTACAAAAACAACATTCAAGGAACTATTCCTCCAGAACTTGGAAACCTGAAGAGTCTCGTTAGCTTGGACTTGTACAACAACAACAT-ATCAGGC
upper sequence: AT3G43740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0009g01210.t01 (Vitis vinifera), 3'ss of exon 2
gtatggaatcatcactcttttgccttttg-attatctgaaaacattt-----acattatcagt-cacacatataacattttgctttgag----tcatatagTGAACTCTACAAAAACGAGATTCAAGGAACTATACCTTCTGAGCTTGGAAATCTGAAGAGTCTAATCAGTTTGGATCTGTACAACAACAATCTCACCGGG
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-tcagcatttttccatgtgttgacaggagtgcaatgcaaaaatgtgctgcggattttattaattcttagatattatttattctttttcactcttcatgtagGGAGCTTTACAAAAACCACATTCAAGGAACTATCCCTGTTGAGCTTGGCAATTTGAGGAGCCTAATCAGCTTGGACTTATATAGCAACAACATCTCAGGGMapped 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|125194671|gb|EL209625.1|EL209625EST: GGGAAGACTTGAACATTTACAATATCT TGAACTCTACAAAAACGAGATTCAAGGAACTATACCTTCTGAGCTTGGAAA
genomic: GGGAAG-CTTGAACATTTACAATATCTgtatggaatc ... agtcatatagTGAACTCTACAAAAACGAGATTCAAGGAACTATACCTTCTGAGCTTGGAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaaacatttacattatcagtcacacatataacattttgctttgagtcatatagTGAACTCTACAAAAACGAGATTCAAGGAACTATACCTTCTGAGCTTGGAAATCTGAAGAGTCTAATCAGTTTGGATCTGTACAACAACAATCTCACCGGG
atataac putative branch site (score: 3)
acatataacatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggaatcatcactcttttgccttttgattatctgaaaacatttacattatcagtcacacatataacattttgctttgagtcatatagTGAACTCTACAAAAACGAGATTCAAGGAACTATACCTTCTGAGCTTGGAAATCTGAAGAGTCTAATCAGTTTGGATCTGTACAACAACAATCTCACCGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA