Sequence
atgc intronic sequence ATGC exonic sequenceCCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATGgtgagaacaatgttacttttgctctttacctaaaaactaacatgttaatttcaaaagcaataacaaaacaagttttgattgaaag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39890.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39890.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA11G38110.1 (Glycine max), 5'ss of exon 2
CCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATGgtgagaacaatgttacttttgctctttacctaaaaacta-----acatgtta------atttcaaaagcaataacaaaacaagttttgat-tgaaag--------------------------------------------------------
|||| ||||| || || || | || |||||||||||||| |||||||||||||||||||||||||| |||| | || ||| ||| | | || | ||| | |||| |||| ||||| ||| | | ||| | || | |
GCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTTTGCAGCTTTGgtaggccatattcctcttcaactcataccacaagatctatttatatttgtttttttgtattttaaaagttatattagatttcacattgttatgtaggcaattttttttaccgttctttgtatgttaaaagtgtgtcgtattttaacttcacag
upper sequence: AT4G39890.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA18G02040.1 (Glycine max), 5'ss of exon 2
CCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATGgtgagaacaatgttacttttgctctttacctaaaaacta---acatgttaatttc-aaaagcaataacaaaacaagttttgat-tgaaag---------------------------------------------------------
|||| ||||| || || || | || |||||||||||||| |||||||||||||||||| ||||||| |||| | || |||| ||| | | || | ||| | || || |||| ||||| ||| | | ||| | || | |
GCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTCTGCAGCTTTGgtaggccatattcctctttaactcatgccacaagacctatttatatttttttttctaaaagttatattagatttcacattgttgtgtaggcactttttttaacccattctttgtatgttaaaattgtttcatattttaacttcacag
upper sequence: AT4G39890.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA08G14390.1 (Glycine max), 5'ss of exon 2
CCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATGgtgagaacaatgttactttt--------------gctctttacctaaaaactaacatgttaattt--caaaagcaataacaaaacaagttttgattgaaag----------------------------------------------------------
| || ||||| || || ||| | || |||||||||||||| |||||| |||| ||||| |||||||| |||| || ||| ||| |||| | | | | | |||| |||| ||| | ||| | | ||| | | | |
GCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCTTGCAGCTTTGgtaggatgaattcctcttcaaatcatatatacaagctcagtctttttatatttgtttgtttatttttcaacaattatattagagtgcacattgctggtatgcctagtaggcattgtttatttttacaatttctgagcttagtatatgttaacttcacag
upper sequence: AT4G39890.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv00s0665g00040.t01 (Vitis vinifera), 5'ss of exon 2
CCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATGgtgagaacaatgttacttttgctctttacctaaaaactaacatgttaat--ttcaaaagcaataa-caaaacaagttttgattgaaag-------------
|||||||||| || |||||| | || ||||| |||||||| || ||||||||| ||||||||||||| |||| || | | || ||| || | | | | | || || ||| | | ||| | ||| |||||| |
GCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTGgt-aggatgcttttccttccacttgtaagcaggtttttcttaattttatgcttccttataagtaatctccacaggttttggcacatccattggtaagcggaMapped 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|116437617|gb|EG480209.1|EG480209EST: CTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATG GGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAG
genomic: CTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATGgtgagaacaa ... tgattgaaagGGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATGgtgagaacaatgttacttttgctctttacctaaaaactaacatgttaatttcaaaagcaataacaaaacaagttttgattgaaag
- - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT