Sequence
atgc intronic sequence ATGC exonic sequenceCATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGTTGGCGCCGGAATCAAAgtacttaatcctaaataagtatcctaattaaatttattttatatggtaacgttacaaaacgaaattaattgcatttatctatatgtatag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G10170.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os10g22450.1 (Oryza sativa), 5'ss of exon 6
CATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGTTGGCGCCGGAATCAAAgtacttaatcctaaataa-gtatcctaattaaatttattttatatggtaacgttacaaaacgaaattaattgcatttatctatatgtatag------
||| |||| |||| ||||||| || || |||||||||||||| ||||||||||||||||| ||||||||||| ||||| || |||||||| ||||| ||| || | || | | | | || | | || | | | ||| | || ||| ||| | || |
CATCAAGAAGAACTCGGTGATCGGCGGCGACGACTTCAAGAGTGGGCAGACCAAGATGAAGTCCGTCCTCGTCGACTTCCTCGTCGGCGCCGGCATCAAGgtatatatgtacatatgatgaactccaactcgggtgatcgcgatcgatgaa---acatgaattggtttgttgtgcatatggaaattggcaatggcag
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os03g09250.3 (Oryza sativa), 5'ss of exon 6
CATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGTTGGCGCCGGAATCAAAgtacttaatcctaaat-aagtatcctaattaaatttat---tttatatggtaacgttacaaaacgaaattaattgcatttatctatatgtatag----------------------
|| |||| |||||| |||| ||||||||||| ||||||||||| ||||| ||||||||||||||| | || |||||||| ||||| || ||||| || |||| || | || || || | | || ||| || | | | | || || || || || ||| ||
TATTAAGAACAACTGCCTGATTGGTGGTGATGATTTCAAGAGTGGACAGACAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtacc-aaccatatatcaaatcctttggctagcttttcgcattgaaacgtcgatattcttccggaaacttttttttatatataacctgataagaactttggcttttgttttcgtag
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G155242_T01 (Zea mays), 5'ss of exon 6
CATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGTTGGCGCCGGAATCAAAgt----acttaatcctaaataagtatcctaattaaat-ttattttatatggtaacgttacaaaacgaaattaattgcatttatctatatgtatag
||||| | ||||||||||| |||||||| |||||||||||||| |||||||||||||| |||||| | ||||||||||||||||| || ||||| || || || || | ||| || || | || |||| | |||||| | || | | |||| | | | ||
TATAAAAAACAACTGCTTGATTGGTGGTGACGACTTCAAGAGTGGACAGACCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacctagtatctctcttctattaagatgaagtgtttttttggcaaatgacgttattgcaataactcttctatattttcattttcatgcag
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G004528_T03 (Zea mays), 5'ss of exon 6
CATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGTTGGCGCCGGAATCAAAgtacttaatcctaaataagtatcctaattaaatttattttatatggtaacgttacaaaacgaaattaattgcatttatctatatgtatag----
|| |||| |||||| ||||||||||||| |||||||||||||| |||||||||||||| || ||||| || ||||| |||||||| || ||||| || |||| | | | ||| | | ||| || || | ||| | | | | || | ||| ||| | ||||||| |
TATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtaca-atttatcaatga--aacctgatatccccccttcgaaatgtttttggcagacgacatacttacaataattcgtgtatatgttcatgcag
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G392513_T02 (Zea mays), 5'ss of exon 4
CATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGTTGGCGCCGGAATCAAAgtacttaatcctaaataagtatcctaattaaatttattttatatggtaacgttacaaaacgaaattaattgcatttatctatatgtatag-------------
|| |||| |||||| ||||||||||||| |||||||||||||| |||||||||||||| || ||||| || || ||||| ||||| || ||||| || |||| | | | ||| | | ||| || || | ||| | | | | | | ||| ||| | |||||| |
TATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCAGTCCTAGTTGAATTCCTAGTTGGTGCTGGAATAAAGgtaca-atttatcaatga--aacctgatatccccccttcgaaatgtttttggcagacggcatacttacaataattcttgcatatgttcattgagagcacctag
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G145638_T02 (Zea mays), 5'ss of exon 2
-CATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGTTGGCGCCGGAATCAAAgtacttaatcctaaataagtatcctaattaaatttattttatatggtaacgttacaaaacgaaattaattgcatttatctatatgtatag----
|| |||| |||||| ||||||||| ||| |||||||||||||| |||||||||||||| || ||||| || |||||||||||||| || |||| || |||| | | | ||| | | ||| || || | ||| | | | | | | ||| ||| | ||||||| |
CTATCAAGAACAACTGCCTGATCGGTGTTGACGACTTCAAGAGTGG-CAGACCAAGATGAAATCAGTCCTGGTTGATTTCCTTGTTGGTGCTAGAATAAAGgtaca-atttatcaatga--aacctgatatccccccttcgaaatgtttttggcagacgtcatacttacaataattcttgtatatgttcatgcag
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G071174_T01 (Zea mays), 5'ss of exon 1
CATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGTTGGCGCCGGAATCAAAgtactta-----atcctaaataagtatcctaat---------taaatttattttatatggta-acgttacaaaacgaaattaattgcatttatctatatgtatag-------------------------------------------------------
|| | |||| || || || |||||||||||||| |||||||||||||||||||| | ||||||||||| || ||||| || || || |||| || || || || |||| || | ||| || | || | ||| | | || | | || |||| || ||| |
---------GAATTCGGTGATAGGAGGCGACGACTTCAAGAGTGGGCAGACCAAGATGAAGTCTGTGTTGGTCGATTTCCTCGTCGGCGCTGGGATTAAGgtacgtaccatcgtcatatatgtatatctctatatataatgctgggattaattaagataatttgtgtttgacattcaagaataatctatccatctttaaatattggaattattaaagattggcacattggataataaggtggatttgttttttcccgtag
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G177461_T01 (Zea mays), 5'ss of exon 6
CATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGTTGGCGCCGGAATCAAAgtac-ttaatcctaaataagtatcctaattaaatttattttatatggtaacgttaca-aaacgaaattaattgca-tttatctatatgtatag-------------------------------------------------------
|||||| | || | |||| || || || ||||| |||||||| |||||||||||||||||||| | ||||||||||| || || || ||||| || |||| || | | || | | ||| | | | | | || || | | | | |||| | | ||||| || |
CATAAAAAAGAATTCGGTGATAGGAGGCGACGACTTTAAGAGTGGGCAGACCAAGATGAAGTCTGTGTTGGTCGATTTCCTCGTCGGTGCTGGAATTAAGgtacattccttgtctattgctgggggcctgggattaagatgaattatttgtctttcacattcaagaataatcgaactttattagcatatcagataatataaggtggattctttttttctttctttttttcgtgtttgtgctgtcgtag
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA18G02210.3 (Glycine max), 5'ss of exon 6
CATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGTTGGCGCCGGAATCAAAgtac-ttaatcctaaataagtatccta--attaaatttatttta--tatggtaa------cgttacaaaa--cgaaattaatt---gcatttatctatatgtatag-------------------------------------------------------
||| ||| ||| ||||| ||||| |||||||||||||||||||||||||| ||||| ||||| | || ||||| ||||| || || || ||||| |||| || | || | | | || || || ||||||| || | || | || || | || |||| |||| ||| || ||||
CATCGCGAGGAACACTTTGATTGGTGGAGATGACTTCAAGAGTGGTCAGACCAAAATGAAATCTGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAGgtacattgttgttatactaatgtcatatcatgggtgttatttttactaggacaatctatcctttgcatgttttgtaaacaatttatgcatcgtgctagatttatatgtcaaaaatggagaaatgagttgattttttcaagtgttctgttgatgattgacag
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA05G31450.4 (Glycine max), 5'ss of exon 3
CATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGTTGGCGCCGGAATCAAAgtacttaatcctaaataagtatcctaattaaatttattttatatg-gtaacgt-tacaaaacgaaattaattgcatttatctatatgtatag-------------
||| ||||| ||| | ||||| || || |||||||| ||||||||||||||||| ||||| ||||| | || ||||||||||| || ||||| ||||| |||| | | | | | | | || ||| |||| | | |||| | | | || || |||| ||| ||| | | ||
CATCAAGAGGAACAGTTTGATTGGAGGAGATGACTTTAAGAGTGGTCAGACCAAAATGAAATCTGTGTTGGTGGATTTCCTTGTGGGGGCCGGCATCAAGgtac---aacttttgttgttgttgttgttgtttttttttttttcatatcacgtgtgctactacaattttattgg--ttaataataaggacagactatcatttgtt
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 5'ss of exon 6
CATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGTTGGCGCCGGAATCAAAgtacttaatcctaaataagtatcctaattaaattta---ttttatat--ggtaacgttacaaa-acgaaattaattgcatttatctatatgtatag-------------------
|| ||||| || | ||||| ||||| ||||| || ||||||||||| ||||||||||| ||||| | || |||||||||||||| || || ||||| ||| | || | | | | || | ||||||| ||||| | ||| | || | |||| | || |||| | ||
TATTAAGAGGAATAGTTTGATTGGTGGGGATGATTTTAAGAGTGGTCAAACCAAGATGAAATCTGTATTGGTGGATTTCCTTGTTGGGGCAGGCATCAAGgtatatcatttttagcatttcctctgttgaaatttagaattttaaagtaaataagtatgcatgtataggattatgtatgaataatgatattgaaagatgatgatggtggtgacag
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S267_10V6.1 (Physcomitrella patens), 5'ss of exon 6
CATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGTTGGCGCCGGAATCAAAgta----------------cttaatcctaaataagtatcctaat----taaatttattttatatggtaacgttacaaaacgaaattaattgcattt----atctatatgtatag
|| ||| || | | || || ||||||||||||||||| || || ||||||||||| ||||| || || || ||||| ||||| || || || || || || | | |||||||| | | || | |||| |||||| || || | | || || | || | || | ||
TGTAGAGAAGAAATCTCTTATTGGCGGTGATGACTTCAAGAGCGGACAAACCAAGATGAAATCTGTGCTTGTGGACTTCCTCGTTGGAGCAGGCATTAAGgtgattcctaagcatctcgtttggttcactggaagtatccggttctctttaaatcgttttctatggtt-tgtcacgatgtatcctgttctgaatctctgaattattgtgcacagMapped 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
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGTTGGCGCCGGAATCAAAgtacttaatcctaaataagtatcctaattaaatttattttatatggtaacgttacaaaacgaaattaattgcatttatctatatgtatag
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG