Sequence
atgc intronic sequence ATGC exonic sequence...tctgtcaatatttgattgtttagcaaagtatgtagtgattgatacaatcgatgtatactgctgaacattttaaaccttgttgtcattgtaaactgaacagTACGAATGCTCAGAGAAGAGTTACAGCTCCTTCAAGAACCTGGGTCCTATGTGGGTGAAGTGGTAAAAGTGATGGGAAAAAACAAGGTCTTGGTTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G20000.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 1
---tctgtcaatatttgattgtttagcaaagtatgtagtgattgatacaatcgatgtatactgctgaacattttaaaccttgttgtcattgtaaactgaacagTACGAATGCTCAGAGAAGAGTTACAGCTCCTTCAAGAACCTGGGTCCTATGTGGGTGAAGTGGTAAAAGTGATGGGAAAAAACAAGGTCTTGGTTAAG
|| | | | | || | | | | |||| | || | | | |||| | | | | | |||| | ||| | || |||| |||||||||| |||||| | ||| | |||||||||||||| || ||||| ||||| ||||| || || ||||| ||| ||||| | || |||
ctatccttgatttgtggagttctacttgatgcatgtgaaatgttatctttttcttctttactatttccctctaaatatgttgt-gcaatttcatcttg--cagTTAGAATGCTCAGGGAAGAGCTGCAGTTGCTTCAAGAACCTGGCTCGTATGTTGGTGAGGTGGTGAAGGTCATGGGTAAATCAAAGGTTCTAGTGAAG
upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 1
tctgtcaatatttgattgtttagcaaagtatgtagtgattgatacaatcgatgtatactgctgaacattttaaaccttg--ttgtcattgtaaactgaacagTACGAATGCTCAGAGAAGAGTTACAGCTCCTTCAAGAACCTGGGTCCTATGTGGGTGAAGTGGTAAAAGTGATGGGAAAAAACAAGGTCTTGGTTAAG
|||| || || | | || | | | || || | || | | | ||||| | || | | || |||| | |||||||||||||| || ||||| |||||||| ||||| || ||||| |||||||| || ||||| ||||||||| ||||| |||||||||
--ggtcacagttgcatagcattaggaattcttttttgctttcctattccttactagaaaaattgaaattttgattaatgaaccttggtggtgttacattcagTGAGGATGCTCAGAGAAGAATTGCAGCTGCTTCAAGAGCCTGGATCATATGTTGGTGAAGTAGTCAAAGTTATGGGAAAATCGAAGGTTTTGGTTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcgatgtatactgctgaacattttaaaccttgttgtcattgtaaactgaacagTACGAATGCTCAGAGAAGAGTTACAGCTCCTTCAAGAACCTGGGTCCTATGTGGGTGAAGTGGTAAAAGTGATGGGAAAAAACAAGGTCTTGGTTAAG
aacattttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctgtcaatatttgattgtttagcaaagtatgtagtgattgatacaatcgatgtatactgctgaacattttaaaccttgttgtcattgtaaactgaacagTACGAATGCTCAGAGAAGAGTTACAGCTCCTTCAAGAACCTGGGTCCTATGTGGGTGAAGTGGTAAAAGTGATGGGAAAAAACAAGGTCTTGGTTAAG
- - - - - - - - tgtttag
- - - - - - - - - - - -caaagta
- - - - - - - - - - - - - - - - - - - - gatacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgctga