Sequence
atgc intronic sequence ATGC exonic sequencegtaagtatttcaagaataccctaccagttatcttcttctccccatctccttagtttttgtaagataatagattatacatgctctgagtagtgggaatgggttctcatctatttttccatgtgtattgcaactttcattctgaccttcttctttaatctgaagCTCTGCTGATATATGGAGTGTTGGGTGCACTGTGATTGAGATGGCTACGGGGAAGCCTCCCTGGAGCGAGCAGTATCAGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06030.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06030.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G098828_T01 (Zea mays), 3'ss of exon 7
gtaagtatttcaagaataccctaccagttatcttcttctccccatctccttagtttttgtaagataatagattatacatgctctgagtagtgggaatgggttctcatctatttttccatgtgtattgcaactttcattctgaccttcttctttaatctgaagCTCTGCTGATATATGGAGTGTTGGGTGCACTGTGATTGAGATGGCTACGGGGAAGCCTCCCTGGAGCGAGCAGTATCAGCAG
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--------------------------------------------------aatgtactgtgatctgaaatagaaaactacttcagaatcgtg---------ttgccttttttttttggtctaatttggcacacccgcccttactattccgttctctc---agTTCTGCAGATATATGGAGTGTAGGGTGCACAGTCATTGAAATGGCCACTGGCAAACCACCATGGAGCCAGCAGTATCAAGAA
upper sequence: AT3G06030.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G39670.1 (Glycine max), 3'ss of exon 7
gtaagtatttcaagaataccctaccagttatcttcttctccccatctccttagtttttgtaagataatagattatacatgctctgagtagtgggaatgggttctcatctatttttccatgtgtattgcaactttcattctgaccttcttctttaatctgaagCTCTGCTGATATATGGAGTGTTGGGTGCACTGTGATTGAGATGGCTACGGGGAAGCCTCCCTGGAGCGAGCAGTATCAGCAG---
|| | | | ||| || || || | | | | | | || | | || | | | || | ||| | ||| || | | | | |||||| |||||||||||||||||| ||||||||||| |||||||| || || |||||||| ||||| | ||||||| |||
----------------------------------------------tcataaacatgagtacgagccta--ttttctttcatttcgatcattagatttgattagagataagccattcttggg----acaa-----aatctaacttg-----tgagttcttagCTCTACTGATATATGGAGTGTTGCATGCACTGTGATAGAGATGGCCACAGGAAAGCCTCCATGGAGTCAACAGTATCCCCAGGAG
upper sequence: AT3G06030.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G28090.1 (Glycine max), 3'ss of exon 7
gtaagtatttcaagaataccctaccagttatcttcttctccccatctccttagtttttgtaagataatagattatacatgctctgagtagtgggaatgggttctcatctatttttccatgtgtattgcaactttcattctgaccttcttctttaatctgaagCTCTGCTGATATATGGAGTGTTGGGTGCACTGTGATTGAGATGGCTACGGGGAAGCCTCCCTGGAGCGAGCAGTATCAGCAG---
| | | ||| | | || || || | ||| | ||| | || | | || | ||| |||| | || | ||| || || | | | | ||||| |||||||||||||||||| ||||||||||| |||||||| || || |||||||| ||||| | ||||||| |||
-----------------------------------------------cataaactttagcatgagcctattttcttcat---ttcagtcattagatttgattag-agatataag-ccattcttgggacag-----aatctaac-----tcgtgattttttagCTCCACTGATATATGGAGTGTTGCATGCACTGTGATAGAGATGGCCACAGGAAAGCCTCCATGGAGTCAACAGTATCCCCAGGAG
upper sequence: AT3G06030.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv05s0020g02910.t01 (Vitis vinifera), 3'ss of exon 7
gtaagtatttcaagaataccctaccagttatcttcttctccccatctccttagtttttgtaagataatagattatacatgctctgagtagtgggaatgggttctcatctatttttccatgtgtattgcaactttcattctgaccttcttctttaatctgaagCTCTGCTGATATATGGAGTGTTGGGTGCACTGTGATTGAGATGGCTACGGGGAAGCCTCCCTGGAGCGAGCAGTATCAGCAG
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-----------------------------------atctgctttgactcctatctccaatgaaataaaaagttattctttct----------------gctccttatcttttgttctttggagctca-----ttaatttggacata------tattttacagCTCTGCTGATATATGGAGTGTTGGATGTACTGTTATTGAGATGGCTACAGGAAAACCTCCTTGGAGCCAGCAATATCAGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctatttttccatgtgtattgcaactttcattctgaccttcttctttaatctgaagCTCTGCTGATATATGGAGTGTTGGGTGCACTGTGATTGAGATGGCTACGGGGAAGCCTCCCTGGAGCGAGCAGTATCAGCAG
ctttcattctgacctt CT-rich tract
ttctttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtatttcaagaataccctaccagttatcttcttctccccatctccttagtttttgtaagataatagattatacatgctctgagtagtgggaatgggttctcatctatttttccatgtgtattgcaactttcattctgaccttcttctttaatctgaagCTCTGCTGATATATGGAGTGTTGGGTGCACTGTGATTGAGATGGCTACGGGGAAGCCTCCCTGGAGCGAGCAGTATCAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG