Sequence
atgc intronic sequence ATGC exonic sequencegtgagctattagtattacatgaatagaggttgttaatgattttgttttagtccctatttttataactgtgatgatttcagGGATCGAGATCGATATGTACAAGGAGATTACCGTTTTAGATATGGCTACTGTCGTCACAATCCTCGAAAGATGGTGAAGACATGGGCTGAAAAAGAACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G37350.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G37350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------------------------------------------------gtgagctat-tagtattacatgaatagaggttgttaatgattttgttttagtcc-ctatttttataactgtgatgatttcagGGATCGAGATCGATATGTACAAGGAGATTACCGTTTTAGATATGGCTACTGTCGTCACAATCCTCGAAAGATGGTGAAGACATGGGCTGAAAAAGAACAG
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gtaaggcatagatctatctacgtattcttttgtaacagggtactttttgacagctactgcagatatgttgattatggatatgttctgtgttttctagttttactaaaacaacttgttctaaaaataacttgcatgtgaacaaactacattattctcttc-ttgcagGGATAGAGACCGATATGTCCATGGAGATTACCGCTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTGAAGACCTGGGCTGAAAAGGAAATG
upper sequence: AT5G37350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G035098_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------------------gtgagctattagtattacatgaatagaggttgt--taatgattttgttttagtccctatttttat-----aactgtg-------atgatttcagGGATCGAGATCGATATGTACAAGGAGATTACCGTTTTAGATATGGCTACTGTCGTCACAATCCTCGAAAGATGGTGAAGACATGGGCTGAAAAAGAACAG
|| | | | |||| | | | |||| ||| |||| | | | | | | || | ||||||| || ||| ||||||| |||| |||||||| ||||||||||||||||||||| |||| ||||| || |||||||| || ||||| ||||| |||||||| || ||| |
gtaagattacaattcaatggttgtttcgaactatggatacttgttgaatcctgatcatgtggttgtgctatttaccttttggtgcttgtataaattatttgatctcaaaacgtgtgcttgttaagaaactgtgtcgttttattattgcagGGATAGAGACCGATATGTCCAAGGAGATTACCGTTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTTAAGACCTGGGCTGAGAAGGAAATG
upper sequence: AT5G37350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G120329_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------------------gtgagctattagtattacatgaatagaggttgt--taatgattttgttttagtccctatttttat-----aactgtg-------atgatttcagGGATCGAGATCGATATGTACAAGGAGATTACCGTTTTAGATATGGCTACTGTCGTCACAATCCTCGAAAGATGGTGAAGACATGGGCTGAAAAAGAACAG
|| | | | |||| | | | |||| ||| |||| | | | | ||| || | ||||||| || ||| ||||||| |||| |||||||| ||||||||||| ||||||||| |||| ||||| || |||||||| || ||||| ||||| ||||||||||| ||| |
gtaagattacaattcaatggttgtttccaactatcgatacttgttgaatcctgatcatgtggtcatgctatttaccttttggtgcttgtataaattatttgatctcaaaacgtatgcttgttaagaaactgtgtcattttattattgcagGGATAGAGACCGATATGTCCAAGGAGATTATCGTTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTTAAGACCTGGGCTGAAAAGGAAATG
upper sequence: AT5G37350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv17s0000g01390.t01 (Vitis vinifera), 3'ss of exon 4
----------------------gtgagctattagtattacatgaatag-aggttgttaatgattt-tgttttagtccctatttttataactgtgatgatttcagGGATCGAGATCGATATGTACAAGGAGATTACCGTTTTAGATATGGCTACTGTCGTCACAATCCTCGAAAGATGGTGAAGACATGGGCTGAAAAAGAACAG
| | ||| ||| || || | || | || || | | | | | | || || | | | | | ||||||| ||||||| |||||||||||||| |||||||| ||| |||| ||||| ||||||||| | || ||||| |||||||||||||| |||||| |
atatctcaatgatgctgatattgcaaatgatttccatttttccaagagtatgtattctatagcttataatgtgattcgtcttgtt----ttctaacaactccagGGATAGAGATCGGTATGTACAAGGAGACTACCGTTTCAGACATGGATACTGCAAGCACAATCCTAGGAAAATGGTAAAGACATGGGCTGAGAAAGAAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaggttgttaatgattttgttttagtccctatttttataactgtgatgatttcagGGATCGAGATCGATATGTACAAGGAGATTACCGTTTTAGATATGGCTACTGTCGTCACAATCCTCGAAAGATGGTGAAGACATGGGCTGAAAAAGAACAG
ttataac putative branch site (score: 2)
ttaatgattttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagctattagtattacatgaatagaggttgttaatgattttgttttagtccctatttttataactgtgatgatttcagGGATCGAGATCGATATGTACAAGGAGATTACCGTTTTAGATATGGCTACTGTCGTCACAATCCTCGAAAGATGGTGAAGACATGGGCTGAAAAAGAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC