Sequence
atgc intronic sequence ATGC exonic sequencegtaatcatctatatattataatgtgatgatctgaacaaatgaaatctgaatgtatattgttcttttaatctgttacagCCGGAGCCAGAGTTTAGACCACCCATGTCTGAAGTGGTGCAAGCATTGGTTGTATTGGTGCAGAGAGCTAACATGAGCAAGAGAACTGTTGGAGTCGGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G14350.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G14350.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os03g08550.2 (Oryza sativa), 3'ss of exon 14
----------gtaatcatctatatat----tataatgtgatgat--ctgaacaaatgaaatctgaatgt----atattgttcttttaatc--tgttacagCCGGAGCCAGAGTTTAGACCACCCATGTCTGAAGTGGTGCAAGCATTGGTTGTATTGGTGCAGAGAGCTAACATGAGCAAGAGAACTGTTGGAGTCGGCT
||| | | | || ||| | | || | || | ||| || | |||||| || || | ||| |||||||||| || ||||| || || ||||| ||||| || |||||||||||||||||| | || ||||| || ||||||| ||||||| | | | |
gtaggatttcaccatcctatgcagatgagctatgcaatactaattacctaatacatggaa-cagaatgtctgaatcttatgaaacaaattcatgttacagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTTCGTCTTGTCCAGAGGGCCAACATGACGAAGAGAATGCTCGACGGAGATA
upper sequence: AT3G14350.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G004572_T01 (Zea mays), 3'ss of exon 15
-----------------------gtaatcatctatatattataatgtgatgatctgaacaaatgaaatctga-atgtatattgttcttttaatctgttacagCCGGAGCCAGAGTTTAGACCACCCATGTCTGAAGTGGTGCAAGCATTGGTTGTATTGGTGCAGAGAGCTAACATGAGCAAGAGAACTGTTGGAGTCGGCT
| ||| | | | | | || | ||| | | | |||| | | ||| ||| | ||||| ||||||||||| ||||| || |||||||| ||||||||||| |||| | || ||||| || ||||||| || ||||| | | | ||
tataagatattcaaaaaatcattggggtcagttgaccccaaaataagggctagctccgcccctgataccagccatgtgaaccaaacctttg--ctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTGCGGCTCGTTCAGAGGGCCAACATGACCAGGAGAATGCTAGATGGCGAGG
upper sequence: AT3G14350.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA03G42360.1 (Glycine max), 3'ss of exon 17
---------gtaatcatctatatattataatgtgatgatctgaacaaatgaaatctgaatgtatat-tgttcttttaatctgttacagCCGGAGCCAGAGTTTAGACCACCCATGTCTGAAGTGGTGCAAGCATTGGTTGTATTGGTGCAGAGAGCTAACATGAGCAAGAGAACTGTTGGAGTCGGCT
| | || | | || | || || || | | | | || | || |||| || | | | |||||||||||||| || ||||||| ||||| |||||||| |||||| |||| ||| |||||| ||||||||||||||||| |||| || | |
gtactgtcagccacgttcccaaaaaattattttgtaaatatggatggaaaatgtttgtgcattcatgtgtttttatttttgggggcagCCGGAGCCAGAATTCCGACCACCAATGTCAGAAGTGGTTCAAGCACTGGTGCGATTAGTGCAGCGAGCTAACATGAGCAAGCGAACATTTAGTAGTAGTG
upper sequence: AT3G14350.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA16G01790.1 (Glycine max), 3'ss of exon 15
---------------------------------------------------------------------------------------------gtaatcatctatatattataa----------tgtgatgatct---gaacaaatgaaatctgaatgtat-attgttc-ttttaatct-------gttacagCCGGAGCCAGAGTTTAGACCACCCATGTCTGAAGTGGTGCAAGCATTGGTTGTATTGGTGCAGAGAGCTAACATGAGCAAGAGAACTGTTGGAGTCGGCT
||| || | | ||| |||| || | | || || | ||| || || || || |||| | | ||||||||||| || || ||||||| ||||| |||||||| |||||| ||||| ||| |||||| || |||||||||||||||| || ||||| |
gtaatgtcagtcgtgtttcatcttaaattttattgttttagtgaataggcagtaaatcacttacttgttttgggcgtctatttgaatttttacacaataattcccaagtgctaagttcaagccttgtggcacccttggggatgaacagcatttacatgcattatcatttattctaattttacttttggggcagCCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCACTGGTTCGATTAGTGCAGCGAACTAACATGAGCAAGAGGACGTTTGGAACTGATC
upper sequence: AT3G14350.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA19G45130.1 (Glycine max), 3'ss of exon 15
------------------------------------------------------------gtaatcatctatatattataatgtgatg-atctgaacaaatgaaatctgaatg-tatattgttcttttaatctgttacagCCGGAGCCAGAGTTTAGACCACCCATGTCTGAAGTGGTGCAAGCATTGGTTGTATTGGTGCAGAGAGCTAACATGAGCAAGAGAACTGTTGGAGTCGGCT
| | | | ||| || || || || | || | | ||||| | | || || |||||||||||||| || ||||||| ||||| |||||||| |||||| |||| | | |||||| ||||||||||||||||| |||| || | |
gtactgtcagacacgttttgattcacccaaaatttattgattttgtaaatatggatggatttgggaaaccacgggggtggatgggaaatatttgtgcatggcttgttcatgtgattttttgtttatattatttggggcagCCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTGCGACTAGTGCAGCGAGCTAACATGAGCAAGCGAACATTTAGTAGTAGTG
upper sequence: AT3G14350.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv09s0002g00150.t01 (Vitis vinifera), 3'ss of exon 15
---------------------------------gtaatcatctatatattataatgtgatgatctgaacaaatgaaatctgaatgtatattgttcttttaatctgttacagCCGGAGCCAGAGTTTAGACCACCCATGTCTGAAGTGGTGCAAGCATTGGTTGTATTGGTGCAGAGAGCTAACATGAGCAAGAGAACTGTTGGAGTCGGCT
| | ||||| | || | || |||| | | | || ||| | || | || | | | || ||||| ||||||||||| | ||||| ||||| ||||||||||||||| |||| | || ||| | || ||||||||||||||||| || | ||
gtaaggtgtttagttaaagtaaagagtgcagatggattcatcatcctgtttcagc-tgctgatg-gtaaagatctgttctctgattttaatattttatcgttttgg-gcagCCTGAGCCAGAGTTCCGGCCACCAATGTCAGAAGTGGTGCAAGCACTGGTGCGGCTAGTCCAGCGGGCAAACATGAGCAAGAGAACCATTAGTAACGAAC
upper sequence: AT3G14350.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: PP1S284_52V6.1 (Physcomitrella patens), 3'ss of exon 16
-----------------------------------------------------------------------------------gtaatcatctatatattataatgtgatgatctgaacaaat--gaaatctgaatgtatattgttcttttaatctgttacagCCGGAGCCAGAGTTTAGACCACCCATGTCTGAAGTGGTGCAAGCATTGGTTGTATTGGTGCAGAGAGCTAACATGAGCAAGAGAACTGTTGGAGTCGGCT-
||| | | | || | ||| | || || | ||||| | ||| ||| | || | | | ||||| ||||||||||||||||| |||||||| |||||||||||| || | || |||| | || |||| | ||||| ||| | | |||||| ||
gtatgctactcgtgttctcaatcaatttcttggcatattcactgataggcattatattcgagtggaaaaccaggtttcagctcttaaagaaagactttttcttcctggatctttagagcagactcgaaatt---acgtaacttgcttcattcctgttctgcagCCAGAGCCAGAGTTTAGACCCCCCATGTCAGAAGTGGTGCAATCACTTGTAAGATTGATACAACGAGCAAGTATGAGTAAGCGCGGT-TTGGAGCTTGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatgatctgaacaaatgaaatctgaatgtatattgttcttttaatctgttacagCCGGAGCCAGAGTTTAGACCACCCATGTCTGAAGTGGTGCAAGCATTGGTTGTATTGGTGCAGAGAGCTAACATGAGCAAGAGAACTGTTGGAGTCGGCT
ttttaat putative branch site (score: 3)
aatgtatattgttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatcatctatatattataatgtgatgatctgaacaaatgaaatctgaatgtatattgttcttttaatctgttacagCCGGAGCCAGAGTTTAGACCACCCATGTCTGAAGTGGTGCAAGCATTGGTTGTATTGGTGCAGAGAGCTAACATGAGCAAGAGAACTGTTGGAGTCGGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG