Sequence
atgc intronic sequence ATGC exonic sequencegtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G15980.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacatttta-ttttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
| |||| ||| | |||| | |||| ||| || | | || | | | |||| | || | | | |||| ||||||| |||||||| || |||||||||||||| | ||||| ||||| || ||||||||||| ||||||||||||
------------------------------------------------gtgagtaattttgttcctggatttaaatttttttttgcgtgtcatttggaatattatgat-gctaaataggatctgctttctta--tttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 4
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
| |||| ||| | ||| | ||| ||| || | | || | | | |||| | ||| | ||||| ||||||| |||||||| || |||||||||||||| | ||||| ||||| || ||||||||||| ||||||||||||
------------------------------------------------gtgagtaattttgttcatggattcaaatttattttgcgtgtcatttggaatattatgat-gctaaatag--gatccgctttcttatttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttg-tcccaattagtgtctttactaactctttactcccatgaa-aaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
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----------------------------------------------------gtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaa-gttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
|| || ||| || | | | || || ||| || | ||||||| | || |||||| ||||| ||| | | | | ||||| || |||||||||| |||||||| ||||||||||||||| | ||||| |||||||||||||||||||| ||||| || |||
---------------------gtaatg-gaatttg----ttaccttattatttcaaacctttttttacattca--tgccatttgaaatgttgtgccactcaaaacatgt-----ttctttg---------------tgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagt-tgaaagttgtcccaattagtgtctttactaactctttactcc---catgaaaaatt-tgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
|| ||| | || |||| | | || | | ||| | | || |||| || | |||| || | || || | | | | ||| |||| || || |||||||||| |||||||| ||||||||||||||| | ||||| |||||||||||||||||||| ||||| || |||
---------------------gtaatgacat-ttgacatttgttgccttata--atttcaaacctggttttgcatttccaatgtgaaggtaatggcatttgacatttgaaatgttgtgccactgaagacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagtt-gtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
| || || ||||| || || |||| || || || ||| | || |||| ||| | || | ||| ||||| |||| |||||||| |||||||| |||| || || || |||||||| |||||||||||| | |||||||||
----------------------------------------------------gtgagtcaaaagtattatttttccttgggtggaaattttgtatgtatgagt-ttaatattaaccttttgttt--atcatgtgtttatagAATGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 14
gtatccaattaccttgtctctgttgtgagaagttagcattcatcactttt-ttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
| || | |||||| | || || ||| | | || || | || | ||| | | | || | |||||| || | | ||||| | ||||||||||| ||||||||||| || | || || || ||| ||||||||||||| ||||||||||||
----------------------------------gtgagtcgttacttttgcttcagcaatggatacccatcatgtgtt---tttactcttttttgccttaacgccactgg-aattgattactcttgtgcctggt--gtagAATGTATATTGGGCTGACAGTGGTGATTTGGTGACAATAGCAAGCGATTCGTCATTCTACATTTTGAAGTACAAT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
| |||| | || ||| | || || | | ||| || || ||| || ||| | || |||| ||| | || | |||| |||| |||| |||||||| |||||||| |||| || || || |||||||| |||||||||||| | |||||||||
-------------------------------------gtgaatcaagtatt----attttttc-ttgggtggaaattttgtatgtaaaatgt----atgagt-ttactattaaccttttcttt--atcatgcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
|| || | || | | | || | | | | || | | ||||| ||||| | ||| | | ||| | | | | ||||| || || |||||||| ||||||||| ||||| | |||||||||||||| ||||||||||| |||||||||||
------------------------gtaagtactttgattaggtgacatctagttatctgctcttttccttcttattc----------gttgtttaatttaattttgttatttatcttgtgt----------------cagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGTGATACATCATTCTACATTCTGAAGTACAAT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
|||| || | ||| | | || | | | || |||| | || ||| | || | ||| ||| ||| || | ||||| || || |||||||| ||||||||| |||| | |||||||||||||| |||||||| ||| |||||||||||
---------------------------gtaagt--gcttgcatgaggtgacatcagctttctgcttttatttcttctt---------actgtttc--ttgttaattttgttaaaatttt-cttgtgt----------cagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttg-cagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
| | | ||| ||| || |||||| || || | | || | | | ||| | ||| | | | || || | || ||||| || || |||||||| ||||||||| ||||| | |||||||| ||||| ||||||||||| |||||||||||
-----------------------------------------gtaagtacttt--gattaggtg---acatttagttatctgctcttttccttcttattcattgtttaatataattttgt-----tattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgtta-cattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
| | | || | || | | | | || | ||| | || | | | || | | ||| ||| | ||| || | ||||| || || |||||||| || ||||||||||| | |||||||||||||| |||||||| ||| | |||||||||
-----------------------------------------gtaagtgcttgcatgaggtggcatcagctttctgcttttatttct---tcttactgtttcttatttttgttaaattttt-cttgtgt----------cagAACCTGTACTGGGCTGATAGCGGTGATTTAGTGACGATTGCTAGTGATACATCATTCTATATCCTTAAGTACAAT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
|| || | || ||| || | | || | | || || ||| || || | | | | | ||| | | || || | | | |||| ||||| || ||||||||||| ||||| ||||| || |||||||| |||||||| ||||| |||||| |||||||||||
------------------------gtaagca-ctaacatg-atggcctgttggctaccgtggtattgt-tttcatgccacactgcagg--aattgattaaatgttccttttttcttttctttttttttcactattt-cagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
|| || | || || | | ||| ||| ||| | | | | || | | | | | | || | || || |||||||||||||||||||| |||||||||||||| || ||||| |||||| | ||||| |||||||| |||||||||
------------------------------------------gcatgttctcaaaaagcttacttcaca----attaccaggt---tttggccacagagaaactaatagttcatttctttgggtggtttcaatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
tactaac putative branch site (score: 0)
atgaaaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG