Sequence
atgc intronic sequence ATGC exonic sequencegtacttaatcctaaataagtatcctaattaaatttattttatatggtaacgttacaaaacgaaattaattgcatttatctatatgtatagCCGACGTCGATTGTCAGTTACAACCATCTTGGGAACAACGACGGCATGAACTTGTCAGCACCTCAAACATTCCGGTCAAAGGAGATATCGAAGAGCAATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G10170.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g09250.3 (Oryza sativa), 3'ss of exon 6
-----------gtacttaatcc--taaataagtatcctaattaaa---tttat-tttatatggtaacgtt---------acaaaacgaaattaattgcatttatctatatgtatagCCGACGTCGATTGTCAGTTACAACCATCTTGGGAACAACGACGGCATGAACTTGTCAGCACCTCAAACATTCCGGTCAAAGGAGATATCGAAGAGCAATG
|| ||||| | || | | | ||| || | || || | || ||| || | || || | || | | | | | | ||||| || || |||||||| |||||||| | ||||| || || ||||||||| | || ||||||||||||||||| || |||||||| || ||||||||||
gtaccaaccatatatcaaatcctttggctagcttttcgcattgaaacgtcgatattcttccggaaacttttttttatatataacctgataagaactttggct-tttgttttcgtagCCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAACCTTTCCGCACCTCAAACATTCCGATCCAAGGAGATCTCCAAGAGCAATG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os10g22450.1 (Oryza sativa), 3'ss of exon 6
gtacttaatcctaaataa-gtatcctaattaaatttattttatatggtaacgttacaaaacgaaattaattgcattt----atctatatgtatagCCGACGTCGATTGTCAGTTACAACCATCTTGGGAACAACGACGGCATGAACTTGTCAGCACCTCAAACATTCCGGTCAAAGGAGATATCGAAGAGCAATG
||| || | || | | | | || | | || | | | | || | | ||||| | || | ||||||||||||| | || |||||||| || || |||||||||||||||||| |||| || || || || |||||||| |||||||| || |||||| |
gtatatatgtacatatgatgaactccaactcgggtgatcgcgatcgatgaaac-atgaattggtttgttgtgcatatggaaattggcaatggcagCCGACGTCGATCGCGAGCTACAACCACCTAGGCAACAACGACGGCATGAACCTGTCGGCGCCGCAGACGTTCCGGTCCAAGGAGATCTCCAAGAGCGGCG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 6
gtacttaatcctaaataagtatcctaattaaatttattttatatggtaacgttacaaaacgaaatta----attgcatttatctatatgtatagCCGACGTCGATTGTCAGTTACAACCATCTTGGGAACAACGACGGCATGAACTTGTCAGCACCTCAAACATTCCGGTCAAAGGAGATATCGAAGAGCAATG
|||| | | | ||| | | ||| || || | ||| | | | | || | ||| | | | | ||| | | | |||| || |||||||| || |||||||| | || |||||||||||||||||| |||| || |||||||||||| |||| |||||||| || |||||||| |
gtaca-atttatcaatga--aacctgatatccccccttcgaaatgtttttggcagacgacatacttacaataattcgtgtatatgttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G145638_T02 (Zea mays), 3'ss of exon 2
gtacttaatcctaaataagtatcctaattaaatttattttatatggtaacgttacaaaacgaaatta----attgcatttatctatatgtatagCCGACGTCGATTGTCAGTTACAACCATCTTGGGAACAACGACGGCATGAACTTGTCAGCACCTCAAACATTCCGGTCAAAGGAGATATCGAAGAGCAATG
|||| | | | ||| | | ||| || || | ||| | | | | | | ||| | | | | ||| | | | |||| || |||||||| || |||||||| | || |||||| ||||||||||| |||| || |||||||||||| |||| |||||||| || |||||||| |
gtaca-atttatcaatga--aacctgatatccccccttcgaaatgtttttggcagacgtcatacttacaataattcttgtatatgttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACAACGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 4
gtacttaatcctaaata-agtatcctaattaaatttattttatatggtaacgttacaaaacgaaattaattgc---------atttatct---atatgtatagCCGACGTCGATTGTCAGTTACAACCATCTTGGGAACAACGACGGCATGAACTTGTCAGCACCTCAAACATTCCGGTCAAAGGAGATATCGAAGAGCAATG
||| || | | | | | || |||||| | || | | | | || | | | |||||| |||| || || | |||| || |||||||| || |||||||| | || |||||||||| ||||||| |||| || |||||||||||| |||| |||||||| || |||||||| |
---cttcatttagcacataagaacttatttaaatgtgttgggcacttaatcaccaaaacataatagaaattgccaagggcacatttccctttcattcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGACATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 6
----gtacttaatcctaaataagtatcctaattaaat-ttattttatatggtaacgttacaaaacgaaattaattgcatttatctatatgtatagCCGACGTCGATTGTCAGTTACAACCATCTTGGGAACAACGACGGCATGAACTTGTCAGCACCTCAAACATTCCGGTCAAAGGAGATATCGAAGAGCAATG
| || || | ||| || || | || |||| | |||||| | || | | |||| | | | |||| || || || || || |||||||| | || |||||||| ||||||||| |||| || |||||||||||| |||| |||||||| || |||||||| |
gtgggaacctagtatctctcttctattaagatgaagtgtttttttggcaaatgacgttattgcaataactcttctatattttcattttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G31450.4 (Glycine max), 3'ss of exon 3
----------gtacttaatcctaaataagtatcctaattaaatttattttatatggtaacgttacaaaacgaaattaattgcatttatctatatgtatagCCGACGTCGATTGTCAGTTACAACCATCTTGGGAACAACGACGGCATGAACTTGTCAGCACCTCAAACATTCCGGTCAAAGGAGATATCGAAGAGCAATG
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gattttttgtatgcttaaactttaattaaaataaaattgaagaacgtgttggggagaagtacattgatgatgttttaattgtctgggtgatgagtgacagCCAACATCTATAGTGAGTTACAACCATCTGGGCAACAATGATGGCATGAATCTCTCAGCCCCTCAAACCTTCCGCTCTAAGGAAATCTCCAAGAGCAATG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 5
----------------------------------------------------------------------------------------------gtacttaatcctaaataagtatcctaattaaatttattttatatggtaacgttacaaaacgaaattaat--tgcatttatct-----atatgt-atagCCGACGTCGATTGTCAGTTACAACCATCTTGGGAACAACGACGGCATGAACTTGTCAGCACCTCAAACATTCCGGTCAAAGGAGATATCGAAGAGCAATG
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gtacaacttttgttgttttgcttactaatactattgctatatcacgtgtgctactacttttattggttaataataaggacagagtatcatttgtatgcttaaactttaattaaaataa-aataaaat--aatgtgttggctaaaaatggagaagtaaattgatgttttaattgtcttggtgatgagtgacagCCAACATCTATAGTGAGTTACAACCATTTGGGAAACAATGATGGCATGAATCTCTCAGCCCCTCAAACCTTCCGCTCGAAGGAAATTTCCAAGAGCAATG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------gtacttaatcctaaataagtatcctaat----taaatttattttatatggtaacgttacaaaacgaaattaattgcattt----atctatatgtatagCCGACGTCGATTGTCAGTTACAACCATCTTGGGAACAACGACGGCATGAACTTGTCAGCACCTCAAACATTCCGGTCAAAGGAGATATCGAAGAGCAATG
|| | | |||||||| | | || | |||| |||||| || || | | || || | || | || | |||| || || ||||| || ||||| ||| | || |||||||| ||||||||||||||||||||||| || || || || |||||||| || || |||||||
gtgattcctaagcatctcgtttggttcactggaagtatccggttctctttaaatcgttttctatggtt-tgtcacgatgtatcctgttctgaatctctgaattattgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S55_204V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------gtacttaatcctaaataagtatcctaattaaatttattttatatggt---------aacgttacaaaa----cgaaattaatt-gcatttatctatatgtatagCCGACGTCGATTGTCAGTTACAACCATCTTGGGAACAACGACGGCATGAACTTGTCAGCACCTCAAACATTCCGGTCAAAGGAGATATCGAAGAGCAATG
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gtgagccaagtgcaatgtgtagaggaataaatgtaataaagccttctaacttgcgctgaatccaacttagaatgtctattttttttggattcaggtgtgtctagaactgaagtttatgctttgcgaagctggaatgattgctatgaaagctttgcactgaacccacaattgttggtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAACTTGTCCGCCCCTCAAACATTCCGTTCCAAGGAGATCTCCAAGAGCAATGMapped 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|125214566|gb|EL228940.1|EL228940EST: CTTGTTGGCGCCGGAATCAAA CCGACGTCGATTGTCAGTTACAACCATCTTGGGAACAACGACGGCATGAAC
genomic: CTTGTTGGCGCCGGAATCAAAgtacttaatc ... atatgtatagCCGACGTCGATTGTCAGTTACAACCATCTTGGGAACAACGACGGCATGAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttatatggtaacgttacaaaacgaaattaattgcatttatctatatgtatagCCGACGTCGATTGTCAGTTACAACCATCTTGGGAACAACGACGGCATGAACTTGTCAGCACCTCAAACATTCCGGTCAAAGGAGATATCGAAGAGCAATG
aaattaattgcattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttaatcctaaataagtatcctaattaaatttattttatatggtaacgttacaaaacgaaattaattgcatttatctatatgtatagCCGACGTCGATTGTCAGTTACAACCATCTTGGGAACAACGACGGCATGAACTTGTCAGCACCTCAAACATTCCGGTCAAAGGAGATATCGAAGAGCAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA