Sequence
atgc intronic sequence ATGC exonic sequencegtaacatccatgaagatacagcatcgaccatttcatattctttcttgcggtctctcattgttagcgtggtgtgtttatccgactgatcattacatgtcaaatccaattatagGCAGTGATCATGGCATCAAAGCGCATGGAGATGGTTGGTTGCTAACTGTTGCTCTAATTGAGGGGGTCGATCTAGCAGCTGTAGATCCAAGCGGGCATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G03370.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g10630.1 (Oryza sativa), 3'ss of exon 2
gtaacatccatgaagatacagcatcgaccatttcatattctttcttgcggtctctcattgttagcgtggtgtgtttatccgactgatcattacatgtcaaatccaattatagGCAGTGATCATGGCATCAAAGCGCATGGAGATGGTTGGTTGCTAACTGTTGCTCTAATTGAGGGGGTCGATCTAGCAGCTGTAGATCCAAGCGGGCATTG
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---------gaaaaaaaactgtattcacc--taagaattgacttttcctgttcttggggataaatcataaatgacaagcatatgtaacctttt-tccctcttccaatattagGTAGTGATCATGGGGTGAAAGCTCATGGTGATGGTTGGTTGCTGACTGTTGCACTTATTGAGGGAAGCGGTGTAGTAGGTTCAGGTACACCTGGCTTGCC
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os06g40570.1 (Oryza sativa), 3'ss of exon 2
-------gtaacatccatgaagatacagcatcgaccatttcatattctttc-ttgcggtctctcattgttagcgtggtgtgtttatccgactgatcattacatgtcaaatccaattatagGCAGTGATCATGGCATCAAAGCGCATGGAGATGGTTGGTTGCTAACTGTTGCTCTAATTGAGGGGGTCGATCT-AGCAGCTGTAGATCCAAGCGGGCATTG
| |||| | ||| | | | | | || ||||| | || || | || || || | | | ||| ||| | || | ||| || ||||||||||| ||||||| ||||| |||||||||||| | |||||||| || |||||||| | | | | | | || || || |||
gtgaaaacttgcatctgttttaatattgtactg-ctactttatattttctccttacagtttcagatgg-------gattaagttaattaacttttttctatgtatca------------gGTAGTGATCATGGGGTCAAAGCTCATGGTGATGGTTGGTTGATGACTGTTGCACTTATTGAGGGCACTGGTATCACTAATTCTAATTCAAAAGAATTATT-
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os06g19400.1 (Oryza sativa), 3'ss of exon 2
gtaacatccatgaagatacagcatcgaccatttcatattcttt-cttgcggtctctcattgttagcgtggtgtgtttatccgactgatcattacatgtcaaatccaattat--agGCAGTGATCATGGCATCAAAGCGCATGGAGATGGTTGGTTGCTAACTGTTGCTCTAATTGAGGGGGTCGATCTAGCAGCTGTAGATCCAAGCGGGCATTG
| ||| | | | || | ||| | |||| | | ||| | | || | | | | ||| | ||||||| | | | ||| ||| ||||||||||| ||||||| || || ||||||||||||| ||||| ||||| ||||| || | || ||||||| | || || | |
---------ctttagaaaaaccttcta----ttcttgttctggacatatatactcccgtgatttatgca-catatgaactaaactttgc-ttacatggtatttgggagtatatagGAAGTGATCATGGAGTCAAAGCACAAGGGAATGGTTGGTTGCTGACTGTCGCTCTGATTGATGGTACCAATTTAGCAGCAACCAAATCATCTGGTTACTC
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G470666_T01 (Zea mays), 3'ss of exon 2
gtaacatccatgaagatacagcatcgaccatt-tcatattctttcttgcggtct-ctcattgttagcgtggtgtgtttatccgactgatcattacatgtcaaatc-caattatagGCAGTGATCATGGCATCAAAGCGCATGGAGATGGTTGGTTGCTAACTGTTGCTCTAATTGAGGGGGTCGATCTAGCAGCTGTAGATCCAAGCGGGCATTG
|| || ||| | || |||| || | | | ||| | | || || | || || | || || ||| |||| ||||||||||| ||||||| |||||||| ||||||||| | ||| |||| || |||||||| || | ||| | || ||
---------------ttatctttaaaactattattattcattttcctgtagcttgcaaattatccattccctatggacatgcatctaatttgcgtttttcttgtctcaacattagGTAGTGATCATGGGGTCAAAGCTCATGGAGACGGTTGGTTGTTGACTATTGCACTTATTGAGGGAAGCGGTGTAGTAAGTGCAG----------------
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G005195_T03 (Zea mays), 3'ss of exon 2
-gtaacatccatgaagatacagcatcgaccatttcatattctttcttgcggtctctcattgttagcgtggtgtgtttatccgactgatcattacatgtcaaatccaattatagGCAGTGATCATGGCATCAAAGCGCATGGAGATGGTTGGTTGCTAACTGTTGCTCTAATTGAGGGGGTCGATCTAGCAGCTGTAGATCCAAGCGGGCATTG---
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tttatttttcttt--gattcaacaaa----acttccaggtttcagatactgttctggataattactcttaca-atcttccttattgatcttt------tggattgtatattagG---TGATCATGGAGTCAAAGCACAAGGGGATGGCTGGTTGCTGACTGTTGCTCTGATGGAGGGAACCAACTTGGCAGCAACCAAATCATCTGGTTACTCTGA
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G12790.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------------------------------------gtaacatccatgaagatacagcatcgaccatttcatattctttcttgcggtctctcattgttagcgtggtgtgttta-tccgactgatcattacatgtcaaatccaattatagGCAGTGATCATGGCATCAAAGCGCATGGAGATGGTTGGTTGCTAACTGTTGCTCTAATTGAGGGGGTCGATCTAGCAGCTGTAGATCCAAGCGGGCATTG
| | | |||| | | | ||| | | | | | || ||| | | ||| |||| | | ||| | || || | || ||| |||| ||||||||||| |||||||| || |||||||| ||||||||||||||||| ||||||| || | | |||| |||| ||| | || ||| |
gtaatctcaagagtgttcagttacttcacacttattgaatttggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcactcttgtcttttgactgtttagtgcccattaacttattttaatgcccatgtttttaattatattgacctttttg-gt--attctaatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------------------------gtaacatccatgaagatacagcatcgaccatttcatattctttcttgcggtctctcattgttagcgtggtgtgttt---atccgactgatcattacatgtcaaatccaattatagGCAGTGATCATGGCATCAAAGCGCATGGAGATGGTTGGTTGCTAACTGTTGCTCTAATTGAGGGGGTCGATCTAGCAGCTGTAGATCCAAGCGGGCATTG
| | | |||| | || | ||| | | | | || ||| | | | |||| | || | ||| |||| || | |||||| |||| ||||||||||| |||||||| || |||||||| ||||||||||||||||| ||||||| || | | |||| |||| ||| | || ||| |
gtaatctcagaatgttcagttacttcacacttcatgaatctggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcgctcttgtcttttgaatgtttagtgcctattaacttattttaatgcctgcgtgtctgtaattatattgaccatttttggt--attccaatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 2
gtaacatccatgaagatacagcatcgaccatttcatattctttcttgcggtctctcattgttagcgtggtgtgtttatccgactgatcattacatgtcaaatccaattatagGCAGTGATCATGGCATCAAAGCGCATGGAGATGGTTGGTTGCTAACTGTTGCTCTAATTGAGGGGGTCGATCTAGCAGCTGTAGATCCAAGCGGGCATTG
|| | || ||| | | | | | | || | | | ||| ||||| | | | || | | | || || | ||||| |||||||||||||||| ||||||| || |||||||| ||| ||||||||||||| | ||||| || || |||||||||| || |||| || |
--aaaaaatattgccatattattttctcaaatctgttattttattggttttttcttcttgttggtttaaaattttgactcttttaattgtt----------ttcaattttagGCAGTGATCATGGAGTCAAAGCACAAGGAGATGGGTGGCTGCTAACTGTTGCCTTGATTGAAGGCAGTAATTTAGCAGCTGTTGACTCAAGTGGATTCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttagcgtggtgtgtttatccgactgatcattacatgtcaaatccaattatagGCAGTGATCATGGCATCAAAGCGCATGGAGATGGTTGGTTGCTAACTGTTGCTCTAATTGAGGGGGTCGATCTAGCAGCTGTAGATCCAAGCGGGCATTG
gactgat putative branch site (score: 3)
aattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacatccatgaagatacagcatcgaccatttcatattctttcttgcggtctctcattgttagcgtggtgtgtttatccgactgatcattacatgtcaaatccaattatagGCAGTGATCATGGCATCAAAGCGCATGGAGATGGTTGGTTGCTAACTGTTGCTCTAATTGAGGGGGTCGATCTAGCAGCTGTAGATCCAAGCGGGCATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG