Sequence
atgc intronic sequence ATGC exonic sequencegtctctttcctaatcagatacaatctctggatcgatataggttctgaagcaaaactctttttaacatttgattgtgtgcagCAAGTATACATGTACTTCAGAGGAAGCGGAAAAGCGGATGATATGAGACGGGATGCTGCAAGAGGAGCCATGAGAGCTGCCATATGAGGCAAATGTAAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G11180.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G11180.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 12
------------------------------------------------------------------------------------------------------------gtctctt--tcctaatcagatacaatctctggat-cgatataggttctgaagcaa-------aactctttttaacatttgattgtgtgcagCAAGTATACATGTACTTCAGAGGAAGCGGAAAAGCGGATGATATGAGACGGGATGCTGCAAGAGGAGCCATGAGAGCTGCCATATGAGGCAAATGTAAAT
|||| | | || | || | | | | | | || ||| |||| ||| | | | |||| ||||||| || |||||||||| |||||||||||| ||||||| |||||||| | ||| |||| || ||||| | || || || ||| | || || | | | | ||
gtcagtcctgcgaataacaaatactccctccgtttcatattataagactttctagcattgcccatattcatatagatgttaataaatctagacatatgtgtctagaaagtcttataatataaaacggagaaagtatgtttttatgaaataaattctcaagtagtctatctgagccgttttgacatttg--tgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGTGATGCAACTAGGGGTGCTATGCGGGCAGCTTTTTAATTATCAGAAAAGA
upper sequence: AT1G11180.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 11
-------------------gtctctttccta-atcagatacaatctctggatcgatataggttctgaagcaaaactctttttaacatttgattgtgtgcagCAAGTATACATGTACTTCAGAGGAAGCGGAAAAGCGGATGATATGAGACGGGATGCTGCAAGAGGAGCCATGAGAGCTGCCATATGAGGCAAATGTAAAT-
|||| | || || | | | | | || | || | | || || || | | | ||||||||||||||||||||||| | ||||| |||||||| | || |||| ||| || || ||| | || || |||| | || | ||| | ||| | |
aggttcaacatagcatggacattcttacatacatttcaatcgtttcttagtcaaattttcattttagatcatgaccattgattgc-tcactcaacatgcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCCGCAGAGATGAAACGTGAGGCGGCACGTGGTGCTCTGAGCTCCGCATTCTGATG-AAACATGCCTT
upper sequence: AT1G11180.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
------------------------------------------------------------------------gtctctttccta---atcagatacaatctctggatcgatataggttctgaagcaaaactcttttta-acatt-tgattgtg-------tgcagCAAGTATACATGTACTTCAGAGGAAGCGGAAAAGCGGATGATATGAGACGGGATGCTGCAAGAGGAGCCATGAGAGCTGCCATATGAGGCAAATGTAAAT
|| ||| || | |||| | | ||| | | || |||| | | | || |||| | | ||| | || || | ||||||||||||||||||||| | ||||| |||||||| | || |||| || || || || | || || ||||| |||| | ||| | |
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagtttcaatta-ttctagaagagagctgttttgagatattattgttctgaacttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctggatcgatataggttctgaagcaaaactctttttaacatttgattgtgtgcagCAAGTATACATGTACTTCAGAGGAAGCGGAAAAGCGGATGATATGAGACGGGATGCTGCAAGAGGAGCCATGAGAGCTGCCATATGAGGCAAATGTAAAT
tttttaacatttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctctttcctaatcagatacaatctctggatcgatataggttctgaagcaaaactctttttaacatttgattgtgtgcagCAAGTATACATGTACTTCAGAGGAAGCGGAAAAGCGGATGATATGAGACGGGATGCTGCAAGAGGAGCCATGAGAGCTGCCATATGAGGCAAATGTAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC