Sequence
atgc intronic sequence ATGC exonic sequencegtatattgtaaagaagcatacttgagatttttgagggatacagacgaaagaagtctaatcgttaacaaattaattatttttcttaccagGTGGCCCTGAAATTTGAGCATCGAAATAGCAAAGGATGCAATTTTGGTCCACCTTACGAGTGGCAAGTGTACAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18190.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 3
gtatattgtaaagaagcatacttgagatttttgagggatacagacgaaagaagtctaatcgttaacaaattaattatttttcttaccagGTGGCCCTGAAATTTGAGCATCGAAATAGCAAAGGATGCAATTTTGGTCCACCTTACGAGTGGCAAGTGTACAA
|||| | | || | || | ||||| |||| | | | | | | |||| | || |||||| | |||| || ||||||| ||||||||||| || ||||||||||||| ||| || || || |||||||| || || ||
---gtttgtcactta-cacattttatgaatttgatggattttttccttaca--taaatccattaaatggtaaa--atttttgt----agGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCTCCATATGAGTGGCAGGTTTATAA
upper sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 3
gtatattgtaaagaagcatacttgagatttttgagggatacagacgaaagaagtctaatcgttaacaaattaattatttttcttaccagGTGGCCCTGAAATTTGAGCATCGAAATAGCAAAGGATGCAATTTTGGTCCACCTTACGAGTGGCAAGTGTACAA
| |||| | |||| | | || | || | | | ||| |||| | || || |||| || ||||||| |||||||| || || ||||||||||||| ||| || || || ||||||||||| || ||
------------gtttgtcacttaacctttt--atgaatttgattcatttttcccttacataaatccaatcaattgtaattttttgtagGTTGCATTGAAATTCGAGCATCGTAACAGTAAAGGATGCAATTATGGCCCCCCATATGAGTGGCAAGTTTATAA
upper sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 3
gtatattgtaaagaagcatacttgagatttttgagggatacagacgaaagaagtctaatcgttaacaaattaattatttt-tcttaccagGTGGCCCTGAAATTTGAGCATCGAAATAGCAAAGGATGCAATTTTGGTCCACCTTACGAGTGGCAAGTGTACAA
| ||| || | | || | ||| | || | || || | | | | || | | ||||| || ||||||||||||| ||||| ||||| || ||||||| ||| || || || ||||||||||| || |
---------gtttatatatagttca---ctctggaagttacttaaaaagataccctcttctatggaagttacactaatacatgaccacagGTTGCTTTGAAATTTGAGCACCGAAACAGCAAGGGCTGCAATTATGGCCCTCCATATGAGTGGCAAGTTTATAG
upper sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 3
gtatattgtaaagaagcatacttgagatttttgagggatacagacgaa-agaagtctaatcgttaacaaattaattatttttcttaccagGTGGCCCTGAAATTTGAGCATCGAAATAGCAAAGGATGCAATTTTGGTCCACCTTACGAGTGGCAAGTGTACAA
| || || | || | | | | | | | | || || | | | | | || || | || ||||| || |||| |||||||| || ||||||||||||||||||| ||| || ||||| ||||||||||| |||||
----gtactattcaaatttttttaaccatatcaaagttttccaatgattagtcacttcagatatgctatttaaagggattcgcataacagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCTCCTTATGAGTGGCAAGTCTACAA
upper sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------gtatattgtaaagaagc-atacttgagatttttgaggga-tacagacgaaagaagtctaatcgttaacaaattaattatttttcttac-----cagGTGGCCCTGAAATTTGAGCATCGAAATAGCAAAGGATGCAATTTTGGTCCACCTTACGAGTGGCAAGTGTACAA
|||| ||| || | | ||| |||| || || || || | |||| || ||||| | | | || || | ||||| || | || ||||| ||||| | ||||| || ||||||| |||||| ||||||||||||||||| |||||
gtactctttactctaattcgttgaggtccggtcgtgtcgtattccgtatagtgccgagggttgtgattatttagcgagtatctttgctttgtgtctggaagt--acaaactgagtcttgttttcgtgctcgcagGTAGCTTTAAAGTTTGAACATCGGAGCAGCAAGGGTTGCAATTATGGTCCTCCTTACGAGTGGCAAGTTTACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggatacagacgaaagaagtctaatcgttaacaaattaattatttttcttaccagGTGGCCCTGAAATTTGAGCATCGAAATAGCAAAGGATGCAATTTTGGTCCACCTTACGAGTGGCAAGTGTACAA
aattaat putative branch site (score: 3)
ttatttttcttacc CT-rich tract
taatcgttaacaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatattgtaaagaagcatacttgagatttttgagggatacagacgaaagaagtctaatcgttaacaaattaattatttttcttaccagGTGGCCCTGAAATTTGAGCATCGAAATAGCAAAGGATGCAATTTTGGTCCACCTTACGAGTGGCAAGTGTACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG