Sequence
atgc intronic sequence ATGC exonic sequencegtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggatataagattttagtgttctggcaacaataattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G05530.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os04g21660.1 (Oryza sativa), 3'ss of exon 5
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggatataagattttagtgttctggcaacaataattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatcca-atttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
| || | | |||| | | | |||||| | ||| | || | | | | | || ||||| || | || || | | | |||| | | ||||| || ||||||| ||||| |||||||||||||| ||||| ||||||||||| || |||||||| ||||| |||||||| ||||| ||||
--------------------------------------------------------------atctttgagctcctctgaaaa--gtttcttagtgct------acatgatttgcct--------ttttttttatgtacgattgagatta-atactggtttctttgtggactcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG
upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 5
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggatataagattttagtgttctggcaacaata-attacatgtgacgagctataatgatacttgattgtaatgacatgatgacat--atccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
| || ||| || || | | ||| | | | | | |||| | || |||| | | | || | | || | ||||||||||| || || || |||||||||||||||||||||||||| ||||| || |||||| | || ||||| || || || |||||||| || || ||||
--------------------------------------------------------------------------------gaagaatattgctttggtccagtgttggtctattttcttcctttattggttcttctgcttgctgctagatacatattaatgtctatgcgaattg-gtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG
upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 5
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggatataag-attttagtgttctggcaacaat--aattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
|||| | | | | ||| | | || | |||| | || || ||| || | | | | || | | | | | | | |||||||| || || || ||||||||||| || || ||||| ||||| ||||| || ||||||||||| ||||| || ||||| ||||| || ||||||||||
------------------------------------------------------------------------------acatatgaacagccttgccttcagaagtctatttatttactatttacttgc-ata-tggttttctagcgcaacaataatcatatttttttgggct-tgcccagATGTTTATCGGTGATGGAGCAAAGCTGGTTCGGGATGCTTTTCAGCTTGCTAAGGAGAAAGCTCCCTGCATCATTTTCATTGATGAGATTGATGCCATTG
upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 5
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtc-tggatataagattttagtgttctggcaacaataattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
| | || | | | |||| | | ||||| | | || | | | | ||| | | ||| | | |||| |||| || | | | | || |||||| ||||| || ||||||||||||||||| ||||| || || |||||||||||||||||||| || ||||| || || ||||| || ||||||||||
--------------------------------------------------------------agacattgcattaccatggaaaatatgttttattctgatgttatct-tgagcacacttta-----tattttcaagtatgatagtaacgatgttcttgctggttca-----------gATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTG
upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G173849_T01 (Zea mays), 3'ss of exon 1
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggatata-agattttagtgttctggcaacaataattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
| | || | | ||| | | ||| || | || | | |||| | ||| || ||| | | | || | | | |||||||| ||||| || ||||||||||||||||| ||||| || || |||||||||||||||||||| || ||||| || || ||||| || |||||||| |
-------------------------------------------------------------------------cgacaaaatggagatattgcattaccatggaaaatctgttt---tattctgagcatactttatattttgaagtagggtagtaacgatgttcttgctg---gttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATCG
upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 5
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggatataagattttagtgttctggcaacaataattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
| || || ||| | | | || || | | || ||| | || | | | | || | |||| | | | | | || | | |||||||||||||| || ||||| |||||||| | ||||| ||||| ||||| || |||||||| |||||||| ||||| || |||||||| ||||||||||
------------------------------------------------------------------------ttttcctgaaata----ctgcgaggtcaattttcagttctattat-tgattatcttttcttagtttaatttagacgaacattaacatctttgtgaattgttt-cagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCTAAGGAGAAAGCCCCGTGCATCATCTTTATTGATGAAATTGATGCCATTG
upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 5
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggata-taagattttagtgttctggcaacaataattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
| || || || | | || | ||| | | || || | || | | || | || | |||| |||||| | | | |||||| | ||||||||||||| ||||| |||||||| ||||| ||||||||||||||||| || |||||||| | || |||||||| || ||||||||||| ||||| ||||
------------------------------------------------------------gtttcctctatttcacttgcacactactaccttatttgtttg-------tattcacgtct------cttgactgggtttggattataatgatctaacc-----tgcaattt-tgtacagATGTTCATAGGAGATGGAGCAAAACTTGTTCGTGATGCCTTTCAACTAGCAAAAGAGAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG
upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 5
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggatataagattttagtgttctggcaacaataattacatgtg-acgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
||| | || || || | | | | ||||||| | | ||| | | ||| |||| || | || || | |||||||||| || |||||||||||||| ||||||| ||||||||||| || || |||||||| |||| |||||||| || ||||||||||| ||||| ||||
--------------------------------------------------------------------------atctatac-tattgttctacttgcgttagatgtttgcatacatgtctatgtgctgcatcagcatttgg----aatggaggaataatctaacctgaaattttacagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTG
upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 5
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggatataagattttagtgttctggcaacaataattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
||| | || | | | | | | | || | | | ||| || || | || |||||| ||||| | | | ||||| | ||||||||||||||||||| |||||||| ||||| ||||| ||||||||||| || ||||| || | || |||||||| || ||||||||||| ||||| ||||
-----------------------------------------------------------------gtttcctctatttcacttgcacact--aatgcctt-----tattgtttatattcatacctcttgactgggttttgattagaatgatctaacc-----tgtaattt-tgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG
upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 3
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggata-taagattttagtg--ttctggcaacaataattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
| | | | | | || ||| || | ||| || || | | | | | |||| ||| ||| | ||| | || ||| ||||| | ||| | || | | |||| |||||| |||||||| ||||||||||| || || |||||||| |||| |||||||| || || |||||||| |||||
-----------------------------------------------------------------atcaatctttttcagctaataattttcttgtgatttttgttgatgaaactcat---tgactg--tatggggattagttattcttatattatgtcttcatattaagG----ATATAAATATGCTTTGGTTCT--AGCAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGC-----
upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 5
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggatataagattttagtgttctggcaacaataattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
|| ||| || || | | || ||||||| || | ||| || |||| | || || | ||||| | | | | ||| |||||||||||||| || || || || |||||||||||||||||||| ||||| ||||||||| |||| ||||| || || ||||||||||| |||||||| |
-------------------------------------------------------------aattctctagttgccatgtagcaattatgttagtgt---------gatgtgtgcattctttgatctattctttta-ttaaatgtaaccaaacaac-------ttggaatgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCTAAAGAGAAATCTCCTTGCATCATTTTTATAGATGAAATTGATGCCATAG
upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 5
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggatataagattttagtgttctggcaacaataattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
|| ||| || || | ||| || | | | | | | || || | ||||||||||| ||||| ||||||||||| || | ||||||||||| || || |||||||| || || ||||| || ||||| |||||| |||| || ||||
--------------------------------------------------------------------------------------------------------------gttctgtgtag-gaactctt----tacctg-tcgggttcttaaactcaagcttctggttcgt-cgcagATGTTCATCGGAGATGGAGCAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTG
upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ15061 (Selaginella moellendorffii), 3'ss of exon 5
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggatataagattttagtgttctggcaacaataattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
|| ||| || || | ||| || | | || | | | || || | | ||||||||||| ||||| ||||||||||| || | ||||||||||| || || |||||||| || || ||||| || ||||| |||||| |||| || ||||
--------------------------------------------------------------------------------------------------------------gttctgtgtag-gaactctt----tacctg-tcgggttgttaaactcaagcttcttgttcgt-tgcagATGTTCATCGGAGATGGAGCAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
acttgat putative branch site (score: 5)
atatccaatttatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggatataagattttagtgttctggcaacaataattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA