Sequence
atgc intronic sequence ATGC exonic sequencegtgagttatttcttcacaacttttaaaaaattagtcttgcttagcttctatagtttctagtgaaatgttttgttgaagttgttgagcttgtatgttgttgaattgtgttggttaaagattgagttagttagtcctcctctgtgtggtttttctttaaggtgtttcattcttgtttatgtagAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G02470.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G02470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g14010.2 (Oryza sativa), 3'ss of exon 1
gtgagttatttcttcacaacttttaaaaaattagtcttgcttagcttctatagtttctagtgaaatgttttgttgaagttgttgagcttgtatgttgttgaattgtgttggttaaagattgagttagttagtcctcctctgtgtggtttttctttaaggtgtttcattcttgtttatgtagAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG
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------------------------------------------------------------------------ccaatgtttcttggctacgatttatttcgattatataacttccatgaaaaaatttccagaaaac----gattgatatgcttctgaattattgtttacat-----tgcagAGAAAGAGAATTTGTGTTTATATGGTCTTCCCAATGAGACATGGGAAGTGAACTTGCCTGCTGAGGAGGTTCCTCCAGAGCTTCCAGAACCAGCTCTGGG
upper sequence: AT2G02470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g34640.1 (Oryza sativa), 3'ss of exon 2
gtgagttatttcttcacaacttttaaaaaattagtcttgcttagcttctatagtttctagtgaaatgttttgttgaagttgttgagcttgtatgttgttgaattgtgttggttaaagattgagttagttagtcctcctctgtgtggtttttctttaaggtgtttcattcttgtttatgtagAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG
|| | |||| | || || | ||| | | | | | | | | | | || | | | | ||| || | || ||| |||||||| ||||| || ||||| || ||||| |||||||| |||| | || | ||||||||||||||| ||| | |||||||||||||||||
------------------------------------------------------------------------------tttctttctttgtcttgcgtagattctgcttgccttttgcataa--caagtgctgcccggacataactcttatgtgtctactaattcctt-tcattcgaacagAAAAGGAGAACTTGTGCCTTTATGGGTACCCTAATGAAACATGGGAAGTTACCTTGCCTGCTGAGGAAGTTCCTCCGGAGATCCCTGAACCAGCTTTAGG
upper sequence: AT2G02470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os04g36730.1 (Oryza sativa), 3'ss of exon 2
gtgagttatttcttcacaacttttaaaaaattagtcttgcttagcttctatagtttctagtgaaatgttttgttgaagttgttgagcttgtatgttgttgaattgtgttggttaaagattgagttagttagtcctcctctgtgtggtttttctttaag-gtgtttcattcttgtttatgtagAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG
|||| | | || |||| || | | || | | | | ||| || || ||| | || | | ||| |||| | || ||| |||||||||||| ||||| ||||||||||| || |||| || |||| || | |||||| | ||| |||||||||||||| || || || ||||| | ||
-------------------------------------------------------------------ttttcaccatacttttat-----tatgcgacaaaacagggcggggc---ggcagggatggtt---ccacccctg-atagtgctgatataaacatgttcc---tttattttgccagAGAAGGAGAACTTGTGCCTCTATGGACTGCCTAATGGAACCTGGGCAGTGACTCTACCAGCTGATGAAGTTCCTCCTGAACTACCAGAGCCAGCCCTCGG
upper sequence: AT2G02470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G107807_T01 (Zea mays), 3'ss of exon 2
gtgagttatttcttcacaacttttaaaaaattagtcttgcttagcttctatagtttctagtgaaatgttttgttgaagttgttgagcttgtatgttgttgaattgtgttggttaaagattgagttagttagtcctcctctgtgtggtttttctttaaggtgtttcattcttgtttatgt-agAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG
| |||| || | |||| | | | ||| | | | || || | | || ||| | | || | | |||| ||| | |||||| |||||| ||||| ||||| || ||||| | ||||||||||| |||||||||| ||| || | ||||||||| |||||||||||||| |||||||| | ||
--------------------------------------------------------------------------actgatgttcag-taacatgtcat-aactagtgacgtgaacatatcagatt------ccatttcctttgttttgtcctgttgacatatttctttcctttttatgccagAGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTTACTCTTCCAGCTGAGGAAGTACCTCCTGAGCTTCCAGAACCAGCACTGGG
upper sequence: AT2G02470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G063864_T01 (Zea mays), 3'ss of exon 2
gtgagttatttcttcacaacttttaaaaaattagtcttgcttagcttctatagtttctagtgaaatgttttgttgaagttgttgagcttgtatgttgttgaattgtgttggttaaagattgagttagttagtcctcctctgtgtggtttttctttaaggtgtttcattcttgtttatgt-agAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG
||| || | | | || ||||| | || | || | | | ||| | | | || | | | | ||||| ||||| |||||| ||||| ||||| || ||||| | ||||||||||| |||||||| | ||| || | ||||||||| |||||||||||||| |||||||| | ||
--------------------------------------------------------------------------------actgatgttcagtaatatgccatattgttgac--atgaacacatcagattccatatttttttgttttgtcccgttgacatagtgctttctttcttatgccagAGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTCACTCTTCCAGCTGAGGAAGTACCTCCTGAGCTTCCAGAACCAGCACTGGG
upper sequence: AT2G02470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G115424_T02 (Zea mays), 3'ss of exon 1
gtgagttatttcttcacaacttttaaaaaattagtcttgcttagcttctatagtttctagtgaaatgttttgttgaagttgttgagcttgtatgttgttgaattgtgttggttaaagattgagttagttagtcctcctctgtgtggtttttctttaaggtgtttcattcttgtttatgtagAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG
| ||| | | | | || || | || | |||| || | | | || | || ||| | | ||| || | ||| | ||||||||| ||||| ||| | ||||||||||| |||||||||||||| || || | || | |||||| ||||||||||| || || || |||||| | ||
-------------------------------------------------------------------------------tcttg-gttcattttcaattaaagcaagccatttta-gatttagagcctgaaacaaccgcaaataccttattcgaaatattattttcttttgttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG
upper sequence: AT2G02470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G153087_T01 (Zea mays), 3'ss of exon 2
gtgagttatttcttcacaacttttaaaaaattagtcttgcttagcttctatagtttctagtgaaatgttttgttgaagttgttgagcttgtatgttgttgaattgtgttggttaaagattgagttagttagtcctcctctgtgtggttt-ttctttaaggtgtttcattcttgtttatgtagAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG
| |||| | | | | ||||| || | | || | | || | | | || | || ||| | | ||| || | ||| |||||||||||| || ||| | ||||||||||| |||||||||||||| | || | || | ||| || || |||||||| || || || |||||| | ||
-------------------------------------------------------------------------------tcttga-ttcatttttgtttgaagtgagctattttaggtttagagt--ctgaaacaactgcaaataccttattcgagatattattttcttttgttttgcacagAGAAGGAGAACTTATGTTTATATGGACTTCCTAATGAGACATGGGAAATAAACTTGCCTGCTGAAGAGGTCCCTCCTGAACTGCCAGAGCCAGCTCTTGG
upper sequence: AT2G02470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G00630.1 (Glycine max), 3'ss of exon 2
gtgagttatttcttcacaacttttaaaaaattagtcttgcttagcttctatagtttctagtgaaatgttttgttgaagttgttgagcttgtatgttgttgaattgtgttggtt--aaagattgagttagttagtcctcctctgtgtggtttttctttaaggt-gtttcattcttgtttatgtagAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG
||| | || | ||| | ||||| ||| || | | | | || || ||| |||| | | | ||||| ||| ||||||||||||||||||||||| ||||| |||||||||| |||||||| || ||| | || ||||||||||| |||||||| |||||||| ||||| |||||
-------------------------------------------------------------------------------tgtcc--ttcataatctcccaaataggaagaacccaaaagaatgattttttgaagtgttatttgcaatgtgttttgttaacattatgttattctcgtt---gtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG
upper sequence: AT2G02470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G40170.1 (Glycine max), 3'ss of exon 2
gtgagttatttcttcacaacttttaaaaaattagtcttgcttagcttctatagtttctagtgaaatgttttgttgaagttgttgagcttgtatgttgttgaattgtgttggttaaagattgagttagttagtcctcctctgtgtggtttttctttaaggtgtttcattcttgtttatgtagAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG
|| || | | || | | | ||| | || |||| | | | || | | |||| |||| || | | | | ||||| ||| ||||||||||||||||||||||| ||||| |||||||||| |||||||| || ||| | || ||||||||||| |||||||| |||||||| ||||| |||||
-------------------------------------------------------------------------tgtccttcataatctcccaaatag--gaagaacccaagagaatgattttttgaagt-gttatttgcaatgtg--ttttattaacattatgttattctcgtt---gtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG
upper sequence: AT2G02470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv12s0035g01980.t01 (Vitis vinifera), 3'ss of exon 2
gtgagttatttcttcacaacttttaaaaaattagtcttgcttagcttctatagtttctagtgaaatgttttgttgaagttgttgagcttgtatgttgttgaattgtgttggttaaagattgagttagttagtcctcctctgtgtggtttttctttaaggtgtttcattcttgtttatgtagAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG
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---------------------------------------------------------------------ttatttta--tattcactttttacattatccatatatatc---ttatgttggcataaatgagtgcaactt------gcttattttggatgt-ttgtaaatttgttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG
upper sequence: AT2G02470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S371_53V6.2 (Physcomitrella patens), 3'ss of exon 2
gtgagttatttcttcacaacttttaaaaaattagtcttgcttagcttctatagtttctagtgaaatgttttgttgaagttgttgagcttgtatgttgttgaattgtgttggt--taaagattgagttagttagtcctcctctgtgtggtttttctttaaggtgtttcattcttgtttat-gtagAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG
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--------------------------------------------------------------------------------gttttcgtagggcaattttgaggta-gttggtgccatgtgttacatcacttagcgctttgttatgtgagtttta---aatgatttttatttttccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGGMapped 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|19875808|gb|AU236639.1|AU236639EST: ATATGGTGAAGTTTTACCAAACGTGTGATCCTG AGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTA
genomic: ATATGGTGAAGTTTTACCAAACGTGTGATCCTGgtgagttatt ... gtttatgtagAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttagtcctcctctgtgtggtttttctttaaggtgtttcattcttgtttatgtagAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG
tttcattcttgttt CT-rich tract
tttttctttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttatttcttcacaacttttaaaaaattagtcttgcttagcttctatagtttctagtgaaatgttttgttgaagttgttgagcttgtatgttgttgaattgtgttggttaaagattgagttagttagtcctcctctgtgtggtttttctttaaggtgtttcattcttgtttatgtagAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT