Sequence
atgc intronic sequence ATGC exonic sequencegtatgttaaacttacgacatcccgatttttcaaaacttaatcaaaataattcctcagtttcagtcttgttcatcttaagatcatgttttcgtttcaagtatgtactttagctgtaacataaatattgcaatcagctatgcatggcacatcgatcatttttgttgacaatctgaatctacagGAGGACCTACTGCTGAATCACGTGGATCCTTAAATCTGAATATCCAATACTGGACAAGTCGAGGTTGGGCATTTGTTGATGTCAATTATGGTGGAAGCAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G36210.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G36210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os06g11190.1 (Oryza sativa), 3'ss of exon 11
gtatgttaaacttacgacatcccgatttttcaaaacttaatcaaaataattcctcagtttcagtcttgttcatcttaagatcatgttttcgtttcaagtatgtactttagctgtaacataaatat---tgcaatcagctatgcatggcacatcgatcatttttgttgacaatct---gaatctacagGAGGACCTACTGCTGAATCACGTGGATCCTTAAATCTGAATATCCAATACTGGACAAGTCGAGGTTGGGCATTTGTTGATGTCAATTATGGTGGAAGCAC
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--------------------------------------------------------------------------------------ttgaattgctaagggaaagcagaacattaaaataaggaaatgtacttttttttaaagaaaggaaatggaa-actcgtattgacattgttgcaattctttagGTGGACCTACAGATGAAGCACGTGGAGTTCTGGATCTTGGTGTTCAGTACTGGACAAGCCGAGGATGGGCATTTGTTGATGTTAACTATGGGGGAAGCAC
upper sequence: AT5G36210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os06g11180.1 (Oryza sativa), 3'ss of exon 11
gtatgttaaacttacgacatcccgatttttcaaaacttaatcaaaataattcctcagtttcagtcttgttcatcttaagatcatgttttcgtttcaagtatgtactttag-ctgtaacataaatattgcaatcagctatg--catggcacatcgatcatttttgttgacaatctgaatctacagGAGGACCTACTGCTGAATCACGTGGATCCTTAAATCTGAATATCCAATACTGGACAAGTCGAGGTTGGGCATTTGTTGATGTCAATTATGGTGGAAGCAC
|| |||| | || | || | |||| | | ||| | || | ||||||| |||| ||| |||| | | | | |||||||||| || || ||| |||||||| | | |||| | | || || |||||||||||||| ||||||| | ||||||| || ||||| ||||||||
---------------------------------------------------------------------------------tgtggtttctgtctaatttggttcgttaggttattgcatccttcttttccatgatcacaatcatggca-atcg--catatttgatattccccacatctttcagGAGGACCAACAGCAGAAACACGTGGAATTCTGGACCTGAGTGTTCAGTATTGGACAAGTCGAGGATGGGCATATCTTGATGTTAACTATGGGGGAAGCAC
upper sequence: AT5G36210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G000231_T01 (Zea mays), 3'ss of exon 9
gtatgttaaacttacgacatcccgatttttcaaaacttaatcaaaataattcctcagtttcagtcttgttcatcttaagatcatgttttcgtttcaagtatgtactttagctgtaacata---aatattgcaatcagctatgcatggcacatcgatcatttttgttgacaatctgaatctacagGAGGACCTACTGCTGAATCACGTGGATCCTTAAATCTGAATATCCAATACTGGACAAGTCGAGGTTGGGCATTTGTTGATGTCAATTATGGTGGAAGCAC
|| ||| | | || | | | | ||||| || | | | | | | || | | || || | | || | | | | | ||| ||||| || | |||| |||| || | |||| | | | || ||||||||||| ||||| ||||||||||||||||| || ||||| |||||| |
----------------------------------------------------------------------------------ttgattttggtccagatgcttgtcaaaagcatcacatagtgaaaaatcttcttaacatt--attataagtttatagcttctttataccacatcattgtttagGTGGACCCACAGATGAAGCACGAGGGGTTCTGGATCTTAGTGTGCAGTACTGGACAAGCCGAGGATGGGCATTTGTTGATGTTAACTATGGGGGAAGCTC
upper sequence: AT5G36210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G42730.1 (Glycine max), 3'ss of exon 11
gtatgttaaacttacgacatcccgatttttcaaaacttaatcaaaataattcctcagtttcagtcttgttcatcttaagatcatgttttcgtttcaagtatgtactttagctgtaacataaatattgcaatcagctatgcatggcacatcgatcatttttgttgacaatctgaatctacagGAGGACCTACTGCTGAATCACGTGGATCCTTAAATCTGAATATCCAATACTGGACAAGTCGAGGTTGGGCATTTGTTGATGTCAATTATGGTGGAAGCAC
| | | || || ||| | | | ||| | | | | ||| | | || || | | | | || ||||| |||| || | |||| ||||| ||||||||| |||||||| ||||| ||| || || |||||||| ||||| ||||||||||| |||||||| |||||||||||||||||
------------------------------------------------------------------taattgttttgg---caaacttt----ttatgcatgggttctcttaatga-gtaatgacttcatacaacgcacttttatattttcattattttgtttgaatattt-------cagGTGGACCAACTGCTGAAACACGTGGAATTTTAAACTTGAGCATTCAGTACTGGACTAGTCGGGGTTGGGCATTCGTTGATGTTAATTATGGTGGAAGCAC
upper sequence: AT5G36210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA18G11480.1 (Glycine max), 3'ss of exon 11
gtatgttaaacttacgacatcccgatttttcaaaacttaatcaaaataattcctcagtttcagtcttgttcatcttaagatcatgttttcgtttcaagtatgtactttagctgtaacataaatattgcaatcagctatgcatggcacatcgatcatttttgttgacaatctgaatctacagGAGGACCTACTGCTGAATCACGTGGATCCTTAAATCTGAATATCCAATACTGGACAAGTCGAGGTTGGGCATTTGTTGATGTCAATTATGGTGGAAGCAC
| | | |||| | || |||||| | ||| | ||| || | ||| || | || | |||| || || ||||| |||| | | |||| ||||| ||| ||| | |||||| |||||| ||| | || |||||||| |||||||||||||| | |||||||| |||||||||||||| ||
---------------------------------------------------------aattacttttgtcaaagttg---tcatgtgtgggttctat-----cactctaatggcttcatgaaacatacactt--ctatatgtgc-------attattttatttgaatgttt-------cagGTGGACCAACTCAAGAAACTCGTGGAATTTTAAATTTGAGCGTTCAGTACTGGACTAGTCGAGGTTGGGCCGTCGTTGATGTTAATTATGGTGGAAGTAC
upper sequence: AT5G36210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv18s0001g11140.t01 (Vitis vinifera), 3'ss of exon 11
gtatgttaaacttacgacatcccgatttttcaaaacttaatcaaaataattcctcagtttcagtcttgttcatcttaagatcatgttttcgtttcaagtatgtactttagctgtaacataaatattgcaatcagctatgcatggcacatcgatcatttttgttgacaatctgaatctacagGAGGACCTACTGCTGAATCACGTGGATCCTTAAATCTGAATATCCAATACTGGACAAGTCGAGGTTGGGCATTTGTTGATGTCAATTATGGTGGAAGCAC
| | | | | | | ||| || ||| || ||| | | | | || | | ||| | ||| | | | ||||||| ||||| |||| |||||||| |||||| ||| |||||| || ||||| |||||||||||||||||||| ||||| |||||||||||||||||
---------------------------------------------------------------------------------aaagatccatgattagctttatacattctctgaaatgaaaaggtagaatttcttctaatattgaattgggatagcatatgtgatgtgtgaaatattgcagGAGGGCCTACAAGTGAAACACGTGGAATTTTAAATTTGAGTATCCAGTATTGGACTAGTCGAGGTTGGGCATTTGTGGATGTGAATTATGGTGGAAGCAC
upper sequence: AT5G36210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv18s0001g11150.t01 (Vitis vinifera), 3'ss of exon 11
gtatgttaaacttacgacatcccgatttttcaaaacttaatcaaaataattcctcagtttcagtcttgttcatcttaagatcatgttttcgtttcaagtatgtactttagctgtaacataaatattgcaatcagctatgcatggcacat-cgatcatttttgttgacaatctgaatctacagGAGGACCTACTGCTGAATCACGTGGATCCTTAAATCTGAATATCCAATACTGGACAAGTCGAGGTTGGGCATTTGTTGATGTCAATTATGGTGGAAGCAC
|||||| | | | | ||| || || | | || || | | | | |||| ||| | || | || | | | || | || ||||||| || || | |||| | | | ||||||| ||| |||||| ||||||||||||||||||||||||||||| ||||| |||||||||||||||||
-----------------------------------------------------------------------------taatcatgatagatgattttctctatacctt--ctcttaaatgaacagtaaattattctatacattgaacttgtaatggtatacatgtgtgatata---ctgcagGAGGGCCGACCGATGAAGCGCACCAAAGCTTAAATTTGAGTATCCAGTACTGGACAAGTCGAGGTTGGGCATTTGTGGATGTGAATTATGGTGGAAGCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaatcagctatgcatggcacatcgatcatttttgttgacaatctgaatctacagGAGGACCTACTGCTGAATCACGTGGATCCTTAAATCTGAATATCCAATACTGGACAAGTCGAGGTTGGGCATTTGTTGATGTCAATTATGGTGGAAGCAC
tgttgac putative branch site (score: 3)
atcattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttaaacttacgacatcccgatttttcaaaacttaatcaaaataattcctcagtttcagtcttgttcatcttaagatcatgttttcgtttcaagtatgtactttagctgtaacataaatattgcaatcagctatgcatggcacatcgatcatttttgttgacaatctgaatctacagGAGGACCTACTGCTGAATCACGTGGATCCTTAAATCTGAATATCCAATACTGGACAAGTCGAGGTTGGGCATTTGTTGATGTCAATTATGGTGGAAGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG