Sequence
atgc intronic sequence ATGC exonic sequencegtaagctatttacatgaataatgttgtttatcagttcttctaaaactcttaacttaatcccagttttcaactttgatgatttcagGGATCGAGATCGATATGTACAAGGAGATTACCGTTTTAGATATGGCTACTGTCGTCACAATCCCCGGAAGATGGTGAAGACATGGGCTGAAAAAGAACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G24990.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G24990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------------------------------gtaagctatttacatgaataatgt-tgtttatcagttcttctaaaact-cttaacttaatcccagttttca------------actttgatgatttc----agGGATCGAGATCGATATGTACAAGGAGATTACCGTTTTAGATATGGCTACTGTCGTCACAATCCCCGGAAGATGGTGAAGACATGGGCTGAAAAAGAACAG
|| | | ||| || | | ||||| |||| | ||||||| ||| ||| | || || || || | ||| |||||| |||| |||||||| || ||||||||||| |||||| |||| ||||| || ||||| ||||| ||||||||||| ||||||||||| ||| |
gtaaggcatagatctatctacgtattcttttgtaacagggtactttttgacagctactgcagatatgttgattatggatatgttctgtgttttctagttttactaaaacaacttgttctaaaaataacttgcatgtgaacaaactacattattctcttcttgcagGGATAGAGACCGATATGTCCATGGAGATTACCGCTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTGAAGACCTGGGCTGAAAAGGAAATG
upper sequence: AT2G24990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G035098_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------------------------gtaagctatttacat--gaataatgttgtttatcagttcttctaaaactcttaacttaatcccagttttcaac-tttgatgatttcagGGATCGAGATCGATATGTACAAGGAGATTACCGTTTTAGATATGGCTACTGTCGTCACAATCCCCGGAAGATGGTGAAGACATGGGCTGAAAAAGAACAG
| ||||||||| | | | | | || | || ||| ||| | ||| | | | | ||| || ||| ||||||| |||| |||||||| ||||||||||||||||||||| |||| ||||| || ||||| ||||| ||||| ||||| |||||||| || ||| |
gtaagattacaattcaatggttgtttcgaactatggatacttgttgaatcctgatcatgtggttgtgctatttaccttttggtgcttgtataaattatttgatctcaaaacgtgtgcttgttaagaaactgtgtcgttttattattgcagGGATAGAGACCGATATGTCCAAGGAGATTACCGTTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTTAAGACCTGGGCTGAGAAGGAAATG
upper sequence: AT2G24990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G120329_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------------------------gtaagctatttacat--gaataatgttgtttatcagttcttctaaaactcttaacttaatcccagttttcaac-tttgatgatttcagGGATCGAGATCGATATGTACAAGGAGATTACCGTTTTAGATATGGCTACTGTCGTCACAATCCCCGGAAGATGGTGAAGACATGGGCTGAAAAAGAACAG
| ||||||||| | | | | | || | || ||| ||| | ||| | | | | ||| || ||| ||||||| |||| |||||||| ||||||||||| ||||||||| |||| ||||| || ||||| ||||| ||||| ||||| ||||||||||| ||| |
gtaagattacaattcaatggttgtttccaactatcgatacttgttgaatcctgatcatgtggtcatgctatttaccttttggtgcttgtataaattatttgatctcaaaacgtatgcttgttaagaaactgtgtcattttattattgcagGGATAGAGACCGATATGTCCAAGGAGATTATCGTTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTTAAGACCTGGGCTGAAAAGGAAATG
upper sequence: AT2G24990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G39750.1 (Glycine max), 3'ss of exon 4
------gtaagctattt-----acatgaataatgttgtttatcagttcttctaaaactcttaacttaat---cccagtttt-caactttgatgatttcagGGATCGAGATCGATATGTACAAGGAGATTACCGTTTTAGATATGGCTACTGTCGTCACAATCCCCGGAAGATGGTGAAGACATGGGCTGAAAAAGAACAG
|||| ||||| |||| | || | || | ||| | || || || | | || | | || ||| |||||||| ||||| ||||||| |||||||| | ||| ||| || |||| ||||| || |||||| |||| ||||| || ||||||||||| |||||| |
taaattgtaatgtatttctactacattgactatagacgaagtttcttgattcaaagttgtttgttttatgaactaaattatatgatcttatcgatatcagGGATAGAGATAGATATGTGCAAGGAGACTTCCGGTTTCGAAATGGATACTGCAAGCATAATCCCAGGAAAATGGTAAAAACATGGGCTGAGAAAGAAATG
upper sequence: AT2G24990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv17s0000g01390.t01 (Vitis vinifera), 3'ss of exon 4
--------gtaa-gctatttacatgaataatgtt-gtttatc----agt---tcttctaaaactcttaacttaatcccagttttcaactttgatgatttcagGGATCGAGATCGATATGTACAAGGAGATTACCGTTTTAGATATGGCTACTGTCGTCACAATCCCCGGAAGATGGTGAAGACATGGGCTGAAAAAGAACAG
| | ||| | ||| || | ||| || ||| | ||||| | || ||| | || | || || | | | | | ||||||| ||||||| |||||||||||||| |||||||| ||| |||| ||||| |||||||| |||| ||||| |||||||||||||| |||||| |
atatctcaatgatgctgatattgcaaatgatttccatttttccaagagtatgtattctatagcttataatgtgattc--gtcttgttttctaacaactccagGGATAGAGATCGGTATGTACAAGGAGACTACCGTTTCAGACATGGATACTGCAAGCACAATCCTAGGAAAATGGTAAAGACATGGGCTGAGAAAGAAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagttcttctaaaactcttaacttaatcccagttttcaactttgatgatttcagGGATCGAGATCGATATGTACAAGGAGATTACCGTTTTAGATATGGCTACTGTCGTCACAATCCCCGGAAGATGGTGAAGACATGGGCTGAAAAAGAACAG
ttaacttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctatttacatgaataatgttgtttatcagttcttctaaaactcttaacttaatcccagttttcaactttgatgatttcagGGATCGAGATCGATATGTACAAGGAGATTACCGTTTTAGATATGGCTACTGTCGTCACAATCCCCGGAAGATGGTGAAGACATGGGCTGAAAAAGAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC