Sequence
atgc intronic sequence ATGC exonic sequencegtctttgtgcttaaccatcataaccggattaaaccagtggttatccatataccgatttgttcacatgttttttttgttatattttgttgtagTATGCATGTAGGAAGACGTTGGCAGATAGTCGTCCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAACCAAATAGACAAGCCTGTTCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G04500.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G04500.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G34250.1 (Glycine max), 3'ss of exon 5
------------------------------------------------gtctttgtgcttaaccat----cataaccggat-taaaccagtggttatccatatac--cgatttgtt--cacatgttttt---tttgttatattttgt---------tgtagTATGCATGTAGGAAGACGTTGGCAGATAGTCGTCCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAACCAAATAGACAAGCCTGTTCAA
|| | | ||| |||| | || || | | || ||| || | | ||||| ||| ||| || || || || ||||||| || | || || |||||||||| || || ||||||||||||| ||||||||||||||||| ||||| ||| | |||||| | || |
gtacagtcaagctccttcccatcttcaaaacagccacatcatcaaacaaaattgaaatcttatcatgttacatatgcatatgcaaggtattccttgcttataaacaaccacttgttattgcatactttcaagttcaactaatgatgcaaccaaatatgcagTATGCCTGCCGCAAAACTCTGGCAGATAGCCGACCTCGAGTTAGAGGAAGGTTTGCAAAGAATGATGACTTTGGAGAAACCAATAGAACTACTAGTAGCA
upper sequence: AT1G04500.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G33390.1 (Glycine max), 3'ss of exon 2
----------gtctttgtgcttaaccatcataaccggattaaacca---gtggttatccatat-----accgatttgt-tcacatgttttt---tttgttatattttgt---------tgtagTATGCATGTAGGAAGACGTTGGCAGATAGTCGTCCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAACCAAATAGACAAGCCTGTTCAA
| | | | | || | | || || | | || ||| | ||| ||| ||| | | ||| ||| || || || || ||||||| || | || || |||||||||| || || |||| |||||||| ||||||||||||||||| ||||| ||| | |||||| | || |
gtacactcaagcttcttcccatcttcaaaacagccatatcatgttacatatgcatatgcttataaacaaccactttttattgcatactttcaagttcaactaatgatgaaaccaaatatgcagTATGCCTGCCGCAAAACTCTGGCAGATAGCCGACCTCGAGTCAGAGGAAGGTTTGCAAAGAATGATGACTTTGGGGAAACCAATAGAACTACAAGTAGCA
upper sequence: AT1G04500.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G21380.1 (Glycine max), 3'ss of exon 4
-------------------------------gtctttgtgcttaac----catcataaccgga-ttaaacca-gtggttatccatataccgatttgttcacatgttttttttgttatattttgttgtagTATGCATGTAGGAAGACGTTGGCAGATAGTCGTCCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAACCAAATAGACAAGCCTGTTCAA
| || ||| | ||| || | | | || | ||| || | || | | | | | | ||| || ||||| | |||||| |||||| || | || || ||||| ||||| || || | ||||||||||| ||||||||||||||||| ||||| |
aaaggatctcgaaattaatggtttggatagaagtatggtacttgatagaacattatggcggaagttgatccatgtagccgaccccac-ctagtgggataagGCGTTGTTGTTGTTGT----TGTTGTTGTATGCTTGCCGCAAAACTTTGGCGGATAGCCGGCCCCGGGTTAGAGGAAGGTTTGCAAAGAATGATGACTTTGGAG------------------------
upper sequence: AT1G04500.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G26990.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------gtctttgtgcttaaccatca--taaccggattaaaccagtggt-tatccatataccgatttgttcacatgtttt----ttttgttatattttgttgtagTATGCATGTAGGAAGACGTTGGCAGATAGTCGTCCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAACCAAATAGACAAGCCTGTTCAA
|| | | | | || | | || || | || | | || | | | || | ||| | |||| | | | || ||||||| || | || || || |||||||| || || | ||||||||||| ||||||||||||||||| ||||| || ||||||||| || |
gtactacatctgaacaccaacattaacaaacaaatttgaaatcttatattatgttatacatgatttccaatctattgcatcaatcaagccttgtgcatattttcaaaattcaactaatgatccaatgttttttaaaaaaaaaatgcagTATGCTTGCCGCAAAACTTTAGCAGATAGCCGGCCCCGGGTTAGAGGAAGGTTTGCAAAGAATGATGAGTTTGGAGAGAGCCATAGACAAGGAAGTAGCA
upper sequence: AT1G04500.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0049g01830.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------gtctttgtgcttaaccatcataaccggattaaaccagtggttatccatataccgatttgttcacatgttttttt----tgttatattt-tgttgtagTATGCATGTAGGAAGACGTTGGCAGATAGTCGTCCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAACCAAATAGACAAGCCTGTTCAA
|| || | | | ||||| | | || || | | | | ||| || | | || | | ||| | | || ||||||||||| | ||||| ||||||| || | ||| ||||||||||||||||||| || |||||||| ||||| || | |||| || |
gttatctctctctctctcgttcttctgctatcattttacattcagatcatgtataggc-atacgtatgataacttaaactttattttcttactaaatgttagaaaaatataataataataatgcagTATGCATGTCGCAAGACACTGGCAGACAGCAGACCACGAGTTAGAGGAAGATTTGCCAAAAATGATGACTTTGGAGAGGCCCCTAGAGCCAGTGGTGGAC
upper sequence: AT1G04500.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S8_144V6.1 (Physcomitrella patens), 3'ss of exon 4
----------gtctttgtgcttaaccatcataaccggattaaaccagtggttatccatataccgatttgttcacatgttttttttgttatattttgttgtagTATGCATGTAGGAAGACGTTGGCAGATAGTCGTCCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAACCAAATAGACAAGCCTGTTCAA-
| | || | || | ||| ||| | || | || || | | || | | ||| | || | | |||| || || | || || |||||||||||||| ||||||||| |||| | |||||||||||| ||| || | || | | | || |
ggccacagcgatttcaagaagaaaaaacaattctctgatcaaatcctcagtgaatgttaaac--aataacccattcttggtctttatgcaatgctcctccagTACGCCTGCCGCAAAACATTGGCAGATAGTCGCCCAAGAGTTCGAGGTCGTTTTGCAAAGAAT-ATGGATGATGAGATGCCGACCACTCTCCTTGGACGTAMapped 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|19878209|gb|AU239040.1|AU239040EST: ATAGGTATATGAAGAAGAGGAACGAGAGGAATTTCAGCAAGAAAATCAAG TATGCATGTAGGAAGACGTTGGCAGATAGTCGTCCAAGAGTTAGAGGAAGA
genomic: ATAGGTATATGAAGAAGAGGAACGAGAGGAATTTCAGCAAGAAAATCAAGgtctttgtgc ... tttgttgtagTATGCATGTAGGAAGACGTTGGCAGATAGTCGTCCAAGAGTTAGAGGAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggttatccatataccgatttgttcacatgttttttttgttatattttgttgtagTATGCATGTAGGAAGACGTTGGCAGATAGTCGTCCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAACCAAATAGACAAGCCTGTTCAA
ttttgtt CT-rich tract
atgttttttttgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctttgtgcttaaccatcataaccggattaaaccagtggttatccatataccgatttgttcacatgttttttttgttatattttgttgtagTATGCATGTAGGAAGACGTTGGCAGATAGTCGTCCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAACCAAATAGACAAGCCTGTTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA