Sequence
atgc intronic sequence ATGC exonic sequencegtaaagtgtttaagattgtaactttcttcttttgtcatttcgttaaatcggggtttctagtgcagAGCTAGAGATGATGAGGGAAAGATTTGCGAAGCTGTTGCTTGGTGAAGACATGTCAGGAAGTGGGAAAGGAGTTTGTACTGCTGTTACTGTGTCAAACTC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G45890.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G45890.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G39560.1 (Glycine max), 3'ss of exon 2
-------------------------gtaaagtgtttaagattgtaactttcttcttttgtc-atttcgttaaatcggggtttctagtgcagAGCTAGAGATGATGAGGGAAAGATTTGCGAAGCTGTTGCTTGGTGAAGACATGTCAGGAAGTGGGAAAGGAGTTTGTACTGCTGTTACTGTGTCAAACTC
|||| | | |||| || |||| | || | || || || || | || ||||| || |||||| |||||||||||| ||||| |||| || ||||||||||| |||||||||||||| ||||| ||||| ||||| | |||||
gttatttgtgaagttttaggacacttagaagtttgaatgattacaaatttcgatagtggttgacttgattttgtccacatt---atagCCGAGCTTGAATTGATGAAGGAAAGATTTGCAAAGCTTCTGCTCGGAGAAGACATGTCTGGAAGTGGGAAAGGTGTTTGCACTGCAGTTACAATCTCAAA---
upper sequence: AT2G45890.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G46690.1 (Glycine max), 3'ss of exon 1
------------------------------------------------------gtaaagtgtttaagattgtaactttcttcttttgtc-atttcgttaaatcggggtttctagtgcagAGCTAGAGATGATGAGGGAAAGATTTGCGAAGCTGTTGCTTGGTGAAGACATGTCAGGAAGTGGGAAAGGAGTTTGTACTGCTGTTACTGTGTCAAACTC
| |||| | | |||| || |||| | || | || || || || | || ||||| || | |||| |||||||||||| ||||| |||| || ||||||||||| |||||||||||||| ||||| ||||| ||||| | |||||
gttggtttgcactttgcatagtttgtgtggttatttgtgaagttttaggacactttgaagtttgaatgattacaaatttcagtagtggttgacttaattttgtccacatt---atagCCGAGCTTGAATTAATGAAGGAAAGATTTGCAAAGCTTCTGCTGGGAGAAGACATGTCTGGAAGTGGGAAAGGTGTTTGCACTGCAGTTACAATCTCAAA---
upper sequence: AT2G45890.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G01560.1 (Glycine max), 3'ss of exon 2
---------gtaaagtgtttaag---attgtaactttcttcttttg-------------tcatttcg---ttaaatcggggtttctag-----tgcagAGCTAGAGATGATGAGGGAAAGATTTGCGAAGCTGTTGCTTGGTGAAGACATGTCAGGAAGTGGGAAAGGAGTTTGTACTGCTGTTACTGTGTCAAACTC--
| || |||| ||| |||||| ||| | || | || | | ||||||| || | | |||||| || |||||||||||||||||||| ||||| | || || ||||||||||| || |||||||||| || || ||||| ||||| || ||||| ||
agacatttatgagagaccttaaacatatttaaacttttttcctatgcgaaaaagtgcaattatatagaaattaaatcaattttgtggggtatttatagagCTTGATATGATGAGGGAAAGATTTGCAAAGCTTCTACTGGGGGAAGACATGTCTGGTGGTGGGAAAGGTGTCTGCACTGCAGTTACAGTATCAAATTCAA
upper sequence: AT2G45890.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0046g02530.t01 (Vitis vinifera), 3'ss of exon 1
-------------------gtaaagtgtttaagattgtaactttcttcttttgtcatttcgttaaatcggggtttctagtgcagAGCTAGAGATGATGAGGGAAAGATTTGCGAAGCTGTTGCTTGGTGAAGACATGTCAGGAAGTGGGAAAGGAGTTTGTACTGCTGTTACTGTGTCAAACTC
| |||| | | | | ||| | | | | || || | ||||| | |||||||| || |||||| |||||||||| | ||||| ||||| |||||||||||||||||||| || ||||| || || ||||| || || | ||||| |
gtgggtccaaacctcatttccggggaagctaaggtctggattctaatctgct-taactaacttgtatttgattttctgg-gcagAGCTTGAACTGATGAAGGAAAGATTTTCCAAGCTTTTGCTGGGTGAAGACATGTCAGGAAGCGGCAAAGGCGTCTGCACTGCGGTCACAATCTCAAATGC
upper sequence: AT2G45890.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S58_274V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------gtaaagtgtttaagattgtaactttcttcttttgt-catttcgttaaatcggggtttctagt---gcagAGCTAGAGATGATGAGGGAAAGATTTGCGAAGCTGTTGCTTGGTGAAGACATGTCAGGAAGTGGGAAAGGAGTTTGTACTGCTGTTACTGTGTCAAACTC
|| || || || | | || | | | | | || | | |||| | |||||| | |||||||||| ||| || ||||| || || |||||||||||||| |||||||| | || ||||| ||||| || || | || | || || |
tgcattactattcgagtgcattttatgatgcatatgtcgtgtacacggctagtgtgatgctgtaatatgtgttgcctgattgtgtcttctgttcttgcagAGGTGGAGATGATGAAGGAGAGGTTTGCAAAACTATTGCTTGGTGAAGATATGTCAGGTGGGGGCAAAGGGGTTTGCACAGCGTTGGCTATATCGAATGC
upper sequence: AT2G45890.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S34_404V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------------------------------gtaaagtgtttaagattgtaactttcttcttt-tgtcatttcgttaaatcggggtttctagtgcagAGCTAGAGATGATGAGGGAAAGATTTGCGAAGCTGTTGCTTGGTGAAGACATGTCAGGAAGTGGGAAAGGAGTTTGTACTGCTGTTACTGTGTCAAACTC
|||| | || | | | ||| | | || || | | || || | |||| | |||||||||| ||| | |||||| ||||||||||| || ||||| |||||||| | || ||||||||||| || || | || | || || |
gtcggtaaacgttatcatcaaaacaaatttctccacaaattcaataagaaatttgactgaatttaagcgcatcgtatgatgcattggctttctccacgtttggactgatagatgcaagcgctgtgttaactgattgaacctg--ttgcttctacagAAGTGGAGATGATGAAGGAGAAATTTGCAAAGCTGTTGCTCGGGGAAGATATGTCAGGTGGGGGTAAAGGAGTTTGCACAGCATTAGCTATATCGAATGCMapped 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|19877047|gb|AU237878.1|AU237878EST: CGGAGATGGAGACGAAGAAGACAGCGACATTGATTCTGCAGAAGATGCAG AGCTAGAGATGATGAGGGAAAGATTTGCGAAGCTGTTGCTTGGTGAAGACA
genomic: CGGAGATGGAGACGAAGAAGACAGCGACATTGATTCTGCAGAAGATGCAGgtaaagtgtt ... tctagtgcagAGCTAGAGATGATGAGGGAAAGATTTGCGAAGCTGTTGCTTGGTGAAGACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagattgtaactttcttcttttgtcatttcgttaaatcggggtttctagtgcagAGCTAGAGATGATGAGGGAAAGATTTGCGAAGCTGTTGCTTGGTGAAGACATGTCAGGAAGTGGGAAAGGAGTTTGTACTGCTGTTACTGTGTCAAACTC
ttgtaac putative branch site (score: 2)
tttct putative PPT
ttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagtgtttaagattgtaactttcttcttttgtcatttcgttaaatcggggtttctagtgcagAGCTAGAGATGATGAGGGAAAGATTTGCGAAGCTGTTGCTTGGTGAAGACATGTCAGGAAGTGGGAAAGGAGTTTGTACTGCTGTTACTGTGTCAAACTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT