Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaactttttgtatttctaaggtagccaggttaatttttgaagtatttgatctgaaactactttcaaacttgaaacagGTTATAAAAGTCATATCAGAGACTCTAGTACCTGCAAATCCTGATATTCTTGATGGAGTGGACGATCTTATGCAGCTTAGTTACTTAAATGAGCCATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G19960.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 2
gtaagtaactt--tttgtatttctaaggtagccaggttaatttttgaagtatt-tgatctgaaactactttcaaacttgaaacagGTTATAAAAGTC-ATATCAGAGACTCTAGTACCTGCAAATCCTGATATTCTTGATGGAGTGGACGATCTTATGCAGCTTAGTTACTTAAATGAGCCATCAG
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gtaagcaacctaatttgctttgttgaaggccttatggttggtttcagagtatgataatctgattctcagtc---atctgatttaagGTACTGAGGTTGAAAACAGAGAGCCTTGAAGCTGCAAATCCTGAAATTCTTGACGGGGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAGCCATCCG
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 2
gtaagtaactttttgtatttctaaggtagccaggt---taatttttg-aagtatt-tgatctgaaactactttcaaacttgaaacagGTTATAAAAGTCATATCAGAGACTCTAGTACCTGCAAATCCTGATATTCTTGATGGAGTGGACGATCTTATGCAGCTTAGTTACTTAAATGAGCCATCAG
|||||| | || | |||||||| ||| | | | |||| || ||| || | || ||| | ||| | |||| | | | | | | | ||| |||| ||||||||||||||| ||||||||||||||||| |||||||||||||| ||||| ||| ||| |||||||
gtaagttgcagatt-tctttctaagatagtctgttctataatcactggaagcatgatcatttgacccccacccttcccttttta-agGTACTGAGATTGAAAACCGAGTGTCTACAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G139583_T02 (Zea mays), 3'ss of exon 2
gtaagtaactttttgtatttctaaggtagccaggttaatttttgaagtatt-tgatctgaaactactttcaaacttgaaacagGTTATAAAAGTCATATCAGAGACTCTAGTACCTGCAAATCCTGATATTCTTGATGGAGTGGACGATCTTATGCAGCTTAGTTACTTAAATGAGCCATCAG
|||||| | || ||| || | | | | |||| || | || ||| ||| | || | ||| | | | | | | |||||| || ||||||||||||||| ||||||||||||||||| || ||||||||||| ||||| ||| ||| |||||||
gtaagttgcagatttcttttaagagtctgttctataatcactggaagcatggtcatttgaccgcccttccctttttaa----gGTACTGAGATTGAAAACAGAGAGCCTTCAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGACCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 3
gtaag-taactttttgtatttct--aaggtagc-caggttaatttttg--aagtatttgatctgaaactactttc--aaacttgaaacagGTTATAAAAGTCATATCAGAGACTCTAGTACCTGCAAATCCTGATATTCTTGATGGAGTGGACGATCTTATGCAGCTTAGTTACTTAAATGAGCCATCAG
||||| ||| || ||||||| | || | || || ||| || ||| ||| | | ||| | ||||| | ||||| | | ||| | | ||||||| |||||||||||||| |||||||||||||| || || ||||| |||||||| ||||||||||| ||||
gtaagataaattacaatatttctcaagagtggtgcatttttggctttactaactatgcagtctcccctctccctgtgggccttattatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGAGTGGATGACCTCATGCAACTTAGTTATTTAAATGAGCCGTCAG
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 3
gtaag-taactttttgtatttctaaggta--gccaggttaatttttgaagtatttgatctgaaactactttca----aacttgaa-acagGTTATAAAAGTCATATCAGAGACTCTAGTACCTGCAAATCCTGATATTCTTGATGGAGTGGACGATCTTATGCAGCTTAGTTACTTAAATGAGCCATCAG
||||| ||| | ||||||| | ||| | ||| |||||| | || | | || | || ||| | | ||||| |||| || | | |||| | | || || || |||||||||||||||||||||||||| || || ||||| || ||||| |||||||||||||| |
gtaagataagtggcaatatttctcaagtaatgttcagttcttttttggtctgattaactgtactcttcccccaccccctcttaatcatagGTTTTAAAGGTGAAAGAGGAGAGTTTGGTGCCAGCTAATCCTGATATTCTTGATGGAGTGGATGACCTCATGCAACTAAGTTATTTAAATGAGCCATCGG
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 1
gtaag-taactttttgtatttctaagg--tagccaggttaatttttg--------aagtatttgatctgaaactactttcaaacttgaa-acagGTTATAAAAGTCATATCAGAGACTCTAGTACCTGCAAATCCTGATATTCTTGATGGAGTGGACGATCTTATGCAGCTTAGTTACTTAAATGAGCCATCAG
|| || ||| || ||||||| ||| | | || ||||||| || ||| ||| | || | | | | | ||||| | ||||| | | ||| | | ||||||| |||||||||||||| |||||||| ||||| || || ||||| |||||||| |||||||| || ||||
gtgagataaattacaatatttctcaggagtggtgcacttcatttttggctttactaactatgcagtctctccccacctgtgggcctaattatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGGGTGGATGACCTCATGCAACTTAGTTATTTAAATGAACCGTCAG
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 2
gtaag-taactttttgtatttct-aaggtagccaggttaatttttgaagtatttgatctgaaactactttcaaacttgaa-acagGTTATAAAAGTCATATCAGAGACTCTAGTACCTGCAAATCCTGATATTCTTGATGGAGTGGACGATCTTATGCAGCTTAGTTACTTAAATGAGCCATCAG
||||| ||| | | ||||||| ||| | ||| ||||| | || | ||| || | ||| | | ||||| | || || | | |||| | | || || || |||||||||||||||||||| ||||| || || ||||| || ||||| ||||| || |||||||
gtaagataagtggctatatttctcaagaatgttcagttctcttttggtctgattaac--agtactctttccccccttaatcatagGTTTTTAAGGTGAAAGAGGAGAGTTTGGTGCCAGCTAATCCTGATATTCTTGATGGGGTGGATGACCTCATGCAACTAAGTTATTTAAACGAACCATCAG
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtaactttttgtatttctaag---------gtagccaggttaatttttgaagta---tttgatctgaaactactttcaaacttgaaacagGTTATAAAAGTCATATCAGAGACTCTAGTACCTGCAAATCCTGATATTCTTGATGGAGTGGACGATCTTATGCAGCTTAGTTACTTAAATGAGCCATCAG
|||||||| | || | | ||| | ||| | | || ||| || | ||| ||| || || ||||| |||| || | | || | || |||||||||| || ||||| ||||| || || || || |||||||| ||||||||||||||||||||||| |
gtaagtaaactaatgcaaacttggatgattgattgtatgtcaatgaatctgttgtttacctttttattttgcactggttttcaattt----tagGTTTTAAAGGTGAATACTGACAGCCTGTTACCTGCAAACCCCGATATACTTGACGGTGTAGATGACCTTATGCAACTTAGTTACTTAAATGAGCCATCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agccaggttaatttttgaagtatttgatctgaaactactttcaaacttgaaacagGTTATAAAAGTCATATCAGAGACTCTAGTACCTGCAAATCCTGATATTCTTGATGGAGTGGACGATCTTATGCAGCTTAGTTACTTAAATGAGCCATCAG
ttaatttttgaagtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaactttttgtatttctaaggtagccaggttaatttttgaagtatttgatctgaaactactttcaaacttgaaacagGTTATAAAAGTCATATCAGAGACTCTAGTACCTGCAAATCCTGATATTCTTGATGGAGTGGACGATCTTATGCAGCTTAGTTACTTAAATGAGCCATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT