Sequence
atgc intronic sequence ATGC exonic sequencegtatgctctcaacttcttttccatcttattttaacttccatgcactttttttttccagttatatgtatgattcaaaggcttgccattactctagttgatgctctctgttaagaggaatgcaaatctttctttctgtgttttgatcattgactcgtttgggtgcagTTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G26570.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 2
gtatgctctcaacttcttttccatcttattttaacttccatgcactttttttttccagttatatgtatgattcaaaggcttgccattactctagttgatgctctctgttaagaggaat---gcaaatctttctttctgtgttttgatcattgactcgtttgggtgcagTTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAG
||| | | ||| | || ||| | | | ||| | || | | ||| || ||| | | ||||| | | | | | || ||| | || | | ||||||| |||||||| || | ||||| || || ||||| || ||||| || |||||||||||||||||||| ||||| || ||||||
------------------------------gtaagtccgccgcattcgccatt---ggttggg-gcgccgtactcctccttccttttgtt---gctgagcctgtctcattgggggaatttgactggtgtgtgtggttgggttggattttgtggccttgtgttgtgcagTCAGCGTGAGCGAGGTCGAGGCGCTGTACGAGCTCTTCAAGAAGATAAGCAGTGCTGTGATTGATGACGGGCTGATTAACAAG
upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
gtatgctctcaacttcttttccatcttattttaacttccatgcactttttttttccagttatatgtatgattcaaaggcttgccattactctagttgatgctctctgttaagaggaatgcaaatctttctttctgtgttttgatcattgactcgtttgggtgcagTTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAG
|| | | | | ||| || | ||| | | | | | | | | ||| | | ||| ||| | | |||| ||| | | | | | ||| ||||||||||||||| || | ||||| | ||||| ||||| ||||| ||||||||||||||||||||||||||||| || ||||||
------------------------------gtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgt-agtaccgtgatcgattgtcttcc---------------gtttgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G173424_T01 (Zea mays), 3'ss of exon 2
gtatgctctcaacttcttttccatcttattttaacttccatgcactttttttttccagttatatgtatgattcaaaggcttgcc-attactctagttgatgctctctgttaagaggaatgcaaatctttctttctgtgttttgatcattgactcgtttgggt---gcagTTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAG
|| | | | | | | | || | | | | | | | | | | | |||| || || | | | | | | | ||||| ||||||||||| | ||||| || || ||||||||||||| |||||||| || || |||||||||||||| || ||||||
------------------------------------------------------------gtaagcccaacccgctctcctctctgctgcttcatcttgcacgcacgggcgaatgaatcgaattgacttctgcgcctggttgggttgcctgtgcttgttgctcctgcagTCAGCGTGAGTGAGGTCGAGGCGCTGTACGAGCTGTTTAAGAGGATCAGCAGCGCCGTCATTGATGATGGGCTGATTAACAAG
upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 2
gtatgctctcaacttcttttccatcttattttaacttccatgcactttttttttccagttatatgtatgattcaaaggcttgcc-attactctagttgatgctctctgttaagaggaatgcaaatctttctttctgtgttttgatcattgactcgtttggg---tgcagTTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAG-----------------
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------------------------------------------------------------gtaagcccaacccgctctcctctctgctgcttcatcttgcacgcacgggcgaatgaatcgaattgacttctgcgcctggttgggttgcctgtgcttgttgctcctgcagTCAGCGTGAGTGAGGTCGAGGCGCTGTACGAGCTGTTTAAGAGGATCAGCAGCGCCGTCATTGATGATGGGCTGATTAACAAGGTCGGCAATGGGTGTCT
upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G007555_T01 (Zea mays), 3'ss of exon 2
gtatgctctcaacttcttttccatcttattttaacttccatgcactttttttttccagttatatgtatgattcaaaggcttgcc--attactctagttgatgctctctgttaagaggaatgcaaatctttctttctgtgttttgatcattgactcgtt-tgggtgcagTTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAG
||| || ||| | | | || | ||| | || | || | | | |||| || || | | | | || || | |||| | || ||| | |||||| |||||||| || | |||||||| || |||||||| ||||| || ||||||||||| || ||||||||||| || ||||||
------------------------------gtaagcatgatctgcttcctctccctggtcgctgcttcatttcgcacgcacggggaatgaattgaattgacgc-ctgcgccttgttcggtctgggtgg--ctgagtgggctttgcctgt--gcttgttgttcctgcagTCAGCGTGAGCGAGGTCGAGGCTCTGTACGAGCTGTTCAAGAAGATAAGCAGTGCTGTCATCGATGATGGGCTGATTAACAAG
upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 1
gtatgctctcaacttcttttccatcttattttaacttccatgcactttttttttccagttatatgtatgattcaaaggcttgccattactctagttgatgctctctgttaagaggaatgcaaatctttctttctgtgttttgatcattgactcgtttgggtgcagTTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAG
|||| || ||||||||||| || || ||||| ||||||||||| |||||||||||||| ||||||||||| || || ||||||
---------------------------------------------------------------------------------------------------------------------------------------------------------------------ttAGTGTAAGTGAAATAGAAGCACTTTATGAACTGTTTAAGAAGATCAGCAGTGCTGTAATTGATGATGGCCTCATCAACAAG
upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 1
gtatgctctcaacttcttttccatcttattttaacttccatgcactttttttttccagttatatgtatgattcaaaggct-tgccattactctagttgatgct--ctctgttaa-gaggaatgcaaatctttctttctgtgttttgatcattgactcgtttgggtgcagTTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAG
| |||| | ||| | || | | || ||| |||| |||| || || || || | || | || || || || | ||||||| || |||||||| ||||| || || |||||||||||||| |||||||| |||||||||||||| || || || ||||||
-------------------------------------------------------------------tcattcctacctaatgctaatagtttgctttctgccaactcttttaatgaaccattaaagcattgtactgaagattgtaattttt--ttctttccaatacagTTAGTGTAAGTGAAATCGAGGCACTATACGAGCTGTTTAAGAAGATCAGCAGCGCTGTGATTGATGACGGTCTGATCAACAAGMapped 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|86019689|gb|DR315435.1|DR315435EST: ACAATCTGGAGGCCTTGGTGACCCTGAACTTCTTGCGAGAGAGACAGTTT TTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCA
genomic: ACAATCTGGAGGCCTTGGTGACCCTGAACTTCTTGCGAGAGAGACAGTTTgtatgctctc ... ttgggtgcagTTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCA
EST:
gi|86019690|gb|DR315436.1|DR315436EST: ACAATCTGGAGGCCTTGGTGACCCTGAACTTCTTGCGAGAGANMCAGTTT TTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCA
genomic: ACAATCTGGAGGCCTTGGTGACCCTGAACTTCTTGCGAGAGAGACAGTTTgtatgctctc ... ttgggtgcagTTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaggaatgcaaatctttctttctgtgttttgatcattgactcgtttgggtgcagTTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAG
cattgac putative branch site (score: 3)
ctcgttt CT-rich tract
aaatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctctcaacttcttttccatcttattttaacttccatgcactttttttttccagttatatgtatgattcaaaggcttgccattactctagttgatgctctctgttaagaggaatgcaaatctttctttctgtgttttgatcattgactcgtttgggtgcagTTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA