Sequence
atgc intronic sequence ATGC exonic sequencegttagatactactgatcctagctacttcttgtgttattattgtgttgaccactcactgttcaataaaattgtaatttgcagAGGCTGGGCATGCTTTAGTTGGTGCACTTATGCCGGAGTATGATCCAGTGGCCAAGATATCGATTATTCCACGTGGCCAAGCTGGTGGGCTCACCTTTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G42270.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os06g51029.1 (Oryza sativa), 3'ss of exon 2
-----gttagatactactgatcctagctactt---cttgtgttattattgtgttgaccactcactgttcaat-----aaaattgtaatttgcagAGGCTGGGCATGCTTTAGTTGGTGCACTTATGCCGGAGTATGATCCAGTGGCCAAGATATCGATTATTCCACGTGGCCAAGCTGGTGGGCTCACCTTTTT
| | || | || | |||| || |||| | |||| | | || || || || || |||||||||||||||| ||||| | |||||||| || ||||| || ||||| || || || ||||| || || ||||| ||||| ||||||||||| ||||| || ||
gtaaatcttgtcaccatattaacttgtgacttgagctgaaattatcctggtgtgcagaggttcctaatccatttttgaacttttcaatttgcagAGGCTGGTCATGCCCTTGTTGGTGCCCTCATGCCTGAATATGACCCTGTTGCTAAGATTTCCATCATTCCTCGTGGTCAAGCTGGTGGACTCACATTCTT
upper sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G126361_T03 (Zea mays), 3'ss of exon 3
-------------gttagatactactgatcctagctacttcttgtgttattattgtgttgaccactca-ctgttcaataaaattgtaatttgcagAGGCTGGGCATGCTTTAGTTGGTGCACTTATGCCGGAGTATGATCCAGTGGCCAAGATATCGATTATTCCACGTGGCCAAGCTGGTGGGCTCACCTTTTT
| ||| || | | | || | || | | | | || | ||||| || ||| |||||| ||||||||| ||||| | || || || || ||||| |||||||||||||| |||||||| || || || || |||||||| |||||||| ||||| || ||
gtaaatgttgtcaaatttatatta-taaccataagtttgactcccgcttacggggctcaggttcctaatctgttgttgaactttggaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAGCCAAGATTTCCATCATCCCTCGTGGCCAGGCTGGTGGACTCACATTCTT
upper sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G02100.1 (Glycine max), 3'ss of exon 2
--------gttagatactactgatcctagctacttcttgtgttattattgtgttgaccactcactgttcaataaaattgtaatttgcagAGGCTGGGCATGCTTTAGTTGGTGCACTTATGCCGGAGTATGATCCAGTGGCCAAGATATCGATTATTCCACGTGGCCAAGCTGGTGGGCTCACCTTTTT
|| || ||| | | | || | ||| || || ||| || | || | || | ||| |||| |||||||||| |||||| |||| ||||| | ||||| || ||||| || || ||||||||||| |||||||| ||||||||||||||||| ||||| |||||
gtatgcattttttttattacccaagtttggtaagtgttggtttgtttttgggtattcaaccttttttttttctatgttg--attttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT
upper sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G02200.1 (Glycine max), 3'ss of exon 2
-------------gttagatactactgatcctagctacttcttgtgttattattgtgttgaccactca--ctgttcaataaaattgtaatttgcagAGGCTGGGCATGCTTTAGTTGGTGCACTTATGCCGGAGTATGATCCAGTGGCCAAGATATCGATTATTCCACGTGGCCAAGCTGGTGGGCTCACCTTTTT
|| || | | | || | || | || | | ||| | ||| || || | || | |||| |||||||||| |||||| |||| ||||| | ||||| || ||||| || || ||||||||||| |||||||| ||||||||||||||||| ||||| |||||
gtatgcattttttttttaatgttcaacacgcaagtttgttaagagttggttggtat-ttgggtattcaaccttttttttcccatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCTGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT
upper sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0001g00190.t01 (Vitis vinifera), 3'ss of exon 2
-------------------gttagatac-tactgatcctagctacttcttgt-gttattattgtgttgaccactcactgttcaataaaattgtaatttgcagAGGCTGGGCATGCTTTAGTTGGTGCACTTATGCCGGAGTATGATCCAGTGGCCAAGATATCGATTATTCCACGTGGCCAAGCTGGTGGGCTCACCTTTTT
|| | ||| | || | | ||| || | ||| | ||| || |||| | | | | | |||||||||||||||||||||| || || |||||||||||||| || ||||| || |||||||||||||| || ||||| ||||||||||| ||||| || ||||||||
gtacataaaagagaacaacacaagctttgtacaggtctctgatgcttgttattgttttgggtgtttta---actctttatgtgtttgcacttgaatttgcagAGGCTGGGCATGCATTGGTCGGTGCACTTATGCCTGAATATGACCCTGTGGCCAAGATATCCATCATTCCCCGTGGCCAAGCAGGTGGTCTTACCTTTTTMapped 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|125209827|gb|EL224781.1|EL224781EST: GAAGAACGCTGTTGTCTCTGAGGAGAAGAAAAGACTTGTTGCTTACCATG AGGCTGGGCATGCTTTAGTTGGTGCACTTATGCC
genomic: GAAGAACGCTGTTGTCTCTGAGGAGAAGAAAAGACTTGTTGCTTACCATGgttagatact ... taatttgcagAGGCTGGGCATGCTTTAGTTGGTGCACTTATGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgtgttattattgtgttgaccactcactgttcaataaaattgtaatttgcagAGGCTGGGCATGCTTTAGTTGGTGCACTTATGCCGGAGTATGATCCAGTGGCCAAGATATCGATTATTCCACGTGGCCAAGCTGGTGGGCTCACCTTTTT
cactcac putative branch site (score: 2)
tgttcaataaaattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagatactactgatcctagctacttcttgtgttattattgtgttgaccactcactgttcaataaaattgtaatttgcagAGGCTGGGCATGCTTTAGTTGGTGCACTTATGCCGGAGTATGATCCAGTGGCCAAGATATCGATTATTCCACGTGGCCAAGCTGGTGGGCTCACCTTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG