Sequence
atgc intronic sequence ATGC exonic sequencegtgagaatgaatctctctctagcgttttctctccatttgtgatttggtatttgtgtctatataataatgttttgatgtttttgttttctacagAAATGGATTCCAGAAGCTGGAGAAGATCAAAGATGCTAATAGGCAGAGTAGGCAGCTGGAAGAACTCACTGACAAAATGCGTGACTGTAAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G35190.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G35190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g50120.2 (Oryza sativa), 3'ss of exon 1
--------gtgagaatgaatctctctctagcgttttctctccatttg--tgatttggtatttgtgtctatataataatgttttgatgtttttgttttctacagAAATGGATTCCAGAAGCTGGAGAAGATCAAAGATGCTAATAGGCAGAGTAGGCAGCTGGAAGAACTCACTGACAAAATGCGTGACTGTAAGAG
| | ||| || ||| | ||| || | | | | | |||| | || | ||||| | || || || || |||||||||| |||||||||||||| |||||||| ||||| ||| | | ||| ||||| || ||||| |||||||| || ||||| || || |||||
tgcaaaaaataaaaataaaa-tctttgtagtgtaatgcggcaaaaagacgggtttgacttagatgatagattgataattaatc--tgcttcatttgtccacagAAATGGGTTCCAGAAGCTGGATAAGATCAAGGATGCCAATCGACGGAGCAGGCAACTCGAAGAGCTCACTGATAAGATGCGGGATTGCAAGAG
upper sequence: AT2G35190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G065105_T02 (Zea mays), 3'ss of exon 1
-----gtgagaatgaatctct---ctctagcgttttctctccatttgtgatttggtatttgtgtctatataataatgttttgatgtttttgttttctacagAAATGGATTCCAGAAGCTGGAGAAGATCAAAGATGCTAATAGGCAGAGTAGGCAGCTGGAAGAACTCACTGACAAAATGCGTGACTGTAAGAG
|| || | || | | || | | | | || | || | | || | | | | || | || || ||| ||||||||| ||||||||||||||||||||||| ||||| || | | || |||||||| ||||| || ||||| || ||||| ||||| |||||
cgctagttggatttggactttggagaccagaccagattgttgacctctggtagcacataggatgcgatcgactgacgcttcc-cgcttgatttgtctgcagAAATGGGTTCCAGAAGCTGGAGAAGATCAAGGATGCCAACCGCCGCAGCAGGCAGCTTGAAGAGCTTACTGATAAGATGCGAGACTGCAAGAG
upper sequence: AT2G35190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G065105_T03 (Zea mays), 3'ss of exon 1
-----gtgagaatgaatctctc---tctagcgttttctctccatttgtgatttggtatttgtgtctatataataatgttttgatgtttttgttttctacagAAATGGATTCCAGAAGCTGGAGAAGATCAAAGATGCTAATAGGCAGAGTAGGCAGCTGGAAGAACTCACTGACAAAATGCGTGACTGTAAGAG-------
|| || | || | | || | | | | || | || | | || | | | | || | || || ||| ||||||||| ||||||||||||||||||||||| ||||| || | | || |||||||| ||||| || ||||| || ||||| ||||| |||||
cgctagttggatttggactttggagaccagaccagattgttgacctctggtagcacataggatgcgatcgactgacgcttcc-cgcttgatttgtctgcagAAATGGGTTCCAGAAGCTGGAGAAGATCAAGGATGCCAACCGCCGCAGCAGGCAGCTTGAAGAGCTTACTGATAAGATGCGAGACTGCAAGAGGTTGCTC
upper sequence: AT2G35190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G15990.1 (Glycine max), 3'ss of exon 1
gtgagaatgaatctctctctagcgttttctctccatttgtgatttggtatt--tgtgtctatataataatgtttt--------------gatgtttttgttttctacagAAATGGATTCCAGAAGCTGGAGAAGATCAAAGATGCTAATAGGCAGAGTAGGCAGCTGGAAGAACTCACTGACAAAATGCGTGACTGTAAGAG
|| |||| || | | || || || || ||| |||| | | | || | | |||||| ||||| ||||| | |||||||||||| |||||| |||||||||| || ||| | ||||| ||||| |||||| ||||||| ||||| || ||| |||| || ||||| |
gtcagaaccttaaccttcttctcattctcattcatttcgtgttttgatgatgttccgttcccacgttgttgttttcttctgatcggtgtaatgttgttgttggttgcagAAATGGATTTCAGAAGTTGGAGAAGATTAAGGATTCGAATAGACAGAGCAGGCAGTTGGAAGACCTCACGGAAAAATTGCGAGAATGTAAACG
upper sequence: AT2G35190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G05710.1 (Glycine max), 3'ss of exon 1
gtgagaatgaatctctctctagcgttttctctccatttgtgatttggtattt-gtgtctatataataatgttttgat------gtttttgttttctacagAAATGGATTCCAGAAGCTGGAGAAGATCAAAGATGCTAATAGGCAGAGTAGGCAGCTGGAAGAACTCACTGACAAAATGCGTGACTGTAAGAG
| |||||| || || | ||||| | ||| | || | ||| | | | || |||| | ||||| | |||||||||||| |||||| ||||||| || || ||| | ||||| |||| |||||| ||||||| ||||| || ||| |||| || ||||| |
----gtcagaatcttcaccttcttcttctcattcattt-cgttttcatgttccattcctacgttgttgttttctgatcggtgtaatgttgttggttgcagAAATGGATTTCAGAAGTTGGAGAAAATTAAGGATTCCAATAGACAGACCAGGCAGTTGGAAGACCTCACCGAGAAATTGCGAGAATGTAAACG
upper sequence: AT2G35190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv02s0012g00140.t01 (Vitis vinifera), 3'ss of exon 1
gtgagaatgaatctctc---tctagcgtttt---ctctccatttgtgatttggtatttgtgtctatataataatgttttgatgtttt-tgt-tttctacagAAATGGATTCCAGAAGCTGGAGAAGATCAAAGATGCTAATAGGCAGAGTAGGCAGCTGGAAGAACTCACTGACAAAATGCGTGACTGTAAGAG
| |||| || | | || | || || | | | | | | | | | | ||| | | | | | || || | ||| ||| ||||| ||||| ||||||||| |||||||||||||||| | | ||||||||| |||||||||||||| || || | || ||| | || ||||||||
aaaacaatgcattatttatgtttaaccattggtgcttgtcctatattacctagcaaat-tatcttctttaaggtaatctaattttctatgtatttttacagTAATGGGTTCCAGAAGTTGGAGAAGATCAAAGACACGAGTAGGCAGAGCAGGCAGCTGGAAGAGCTTACGGGGAAGATGAGAGAGTGTAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgatttggtatttgtgtctatataataatgttttgatgtttttgttttctacagAAATGGATTCCAGAAGCTGGAGAAGATCAAAGATGCTAATAGGCAGAGTAGGCAGCTGGAAGAACTCACTGACAAAATGCGTGACTGTAAGAG
ttttgat putative branch site (score: 4)
tgtttttgttttct CT-rich tract
tatataataatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagaatgaatctctctctagcgttttctctccatttgtgatttggtatttgtgtctatataataatgttttgatgtttttgttttctacagAAATGGATTCCAGAAGCTGGAGAAGATCAAAGATGCTAATAGGCAGAGTAGGCAGCTGGAAGAACTCACTGACAAAATGCGTGACTGTAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC