Sequence
atgc intronic sequence ATGC exonic sequencegtatctatctatcttccttttcctccattgttccctcatgaaaaaaaaaacacaaagagaacatctttcttctccttttcagATATGTAACTACTCATCCATGGATGGAGTTTTGTATTGCAAGACCCATTTTGAACAGCTCTTCAAAGAATCTGGAAATTTCAGCAAGAATTTCCAAACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G61230.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G61230.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g42820.1 (Oryza sativa), 3'ss of exon 1
--------gtatc-tatctatcttccttttcctccattgttccctcatgaaaaaaaaaacacaaagagaacatctttcttct------------ccttttcagATATGTAACTACTCATCCATGGATGGAGTTTTGTATTGCAAGACCCATTTTGAACAGCTCTTCAAAGAATCTGGAAATTTCAGCAAGAATTTCCAAACAG
||| ||| ||| || | || | || | || || ||| | |||| |||| | | | | ||||| ||||||||||| || |||||||| || |||| |||||||| || ||||| |||||||||||||| | || | ||| ||||| ||| ||
gtatgtatatatggcatcgatcggccctgcaacatgttcagtttttattaggtaattaaatcaactatcacatttttcgttcaaaacatttacgcatctgcagATGTGTAACTACTCTTCGATGGATGGTGTCCTGTACTGCAAGACGCACTTTGAGCAGCTCTTCAAAGAGACGGGGAGCTTCTCAAAGAAATTCTCGCAAG
upper sequence: AT3G61230.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os10g35930.1 (Oryza sativa), 3'ss of exon 1
----------------------------------gtatct-atctatcttccttttcctccattgttccctcatgaaaaaaaaaacaca-aagagaacatctttcttctccttttcagATATGTAACTACTCATCCATGGATGGAGTTTTGTATTGCAAGACCCATTTTGAACAGCTCTTCAAAGAATCTGGAAATTTCAGCAAGAATTTCCAAACAG
|| | ||| | || | || ||| | || | | || || || | | | | ||| ||||| || | ||| || ||||||||||| ||| | || ||||||||||||||||| ||||| ||||| ||| | || | |||| ||||| |||| |||
gtatgcactcttcttggtgtctgcactccttgatgtgaatgatcagttttttatgctcttcatgatgttaaaatattatatgttactcatgagctgatgtgaattgttctatttccagATGTGCAGCTATTCGTCCATGGATGGGGTTCTTTACTGCAAGACCCATTTTGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAG
upper sequence: AT3G61230.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G134752_T02 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------gtatctatctatcttccttttcctccattgttccctcatgaaaaaaaaaacacaaa-----gagaacatctttct---------------tctccttttcagATATGTAACTACTCATCCATGGATGGAGTTTTGTATTGCAAGACCCATTTTGAACAGCTCTTCAAAGAATCTGGAAATTTCAGCAAGAATTTCCAAACAG
| ||| || | || | | || | | | ||| | || || || || ||||| |||||| | |||| | | |||||| |||||||| || ||| |||| |||||||| || ||||||||||||||||| || | || || ||| |||||| ||||||
gtacgcatgccgcatggcccccctcaagccctcaacactcttactcctcacgcgcatttgccttcctgtgaatcctgtgatacgcattcatcccgatagatgaca-atgtagggaataatacgggctcatattaattcttttctgcatccgtcggtcgatctcctctctagATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTTGAACAGCTCTTCAAGGAGACGGGGAACTTCTCCAAGAAATTCCAAG---
upper sequence: AT3G61230.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G170034_T02 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------------------------gtatctatctatcttccttttcctccattgttccctcatgaaaaaaaaaacacaaagagaacatctttcttc--------------tccttttcagATATGTAACTACTCATCCATGGATGGAGTTTTGTATTGCAAGACCCATTTTGAACAGCTCTTCAAAGAATCTGGAAATTTCAGCAAGAATTTCCAAACAG
| | || | || || | || | | | || | | ||| | || || || || | ||||| | | |||||| |||||||| || || |||| |||||||| || ||||||||||||||||| || | || | ||| ||||| || |||
gtatgcatgcgtggcctgagctcaactccgcatgcgcattcgccctgcttgcgatgtgtgcggcaatgcgctaatgctcatttgcatcgaaagaaacgaagctttgtttgattcggttcagatcatctcgacagatgaacatgtagaaatacggtctcattttttcatttctgcatgcgtctcctccagATTAGCAGCTACTCTTCCATGGACGGCGTCCTGTACTGCAAGACGCACTTTGAACAGCTCTTCAAGGAGACAGGGACCTTCTCAAAGAACTTTCAAGGTA
upper sequence: AT3G61230.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G170034_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------------------------gtatctatctatcttccttttcctccattgttccctcatgaaaaaaaaaacacaaagagaacatctttcttc--------------tccttttcagATATGTAACTACTCATCCATGGATGGAGTTTTGTATTGCAAGACCCATTTTGAACAGCTCTTCAAAGAATCTGGAAATTTCAGCAAGAATTTCCAAACAG
| | || | || || | || | | | || | | ||| | || || || || | ||||| | | |||||| |||||||| || || |||| |||||||| || ||||||||||||||||| || | || | ||| ||||| || |||
gtatgcatgcgtggcctgagctcaactccgcatgcgcattcgccctgcttgcgatgtgtgcggcaatgcgctaatgctcatttgcatcgaaagaaacgaagctttgtttgattcggttcagatcatctcgacagatgaacatgtagaaatacggtctcattttttcatttctgcatgcgtctcctccagATTAGCAGCTACTCTTCCATGGACGGCGTCCTGTACTGCAAGACGCACTTTGAACAGCTCTTCAAGGAGACAGGGACCTTCTCAAAGAACTTTCAAG---
upper sequence: AT3G61230.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G01590.1 (Glycine max), 3'ss of exon 1
-------------------gtatctatctatcttccttttcctccattgttccctcatgaaaaaaaaaacacaaagagaacatctttcttctccttttcagATATGTAACTACTCATCCATGGATGGAGTTTTGTATTGCAAGACCCATTTTGAACAGCTCTTCAAAGAATCTGGAAATTTCAGCAAGAATTTCCAAACAG
||| || | | | || | | || | || | || | | || | | | |||||| | | ||||| || ||||||||| || | ||||||||||| |||||||||||||| ||||| ||||||||||||||||||||||| ||
gaagtaaattgatatgatactattcattcaaataaaatgtcattttaacattgttcctaaattcgggggtgccaatgatata-ctacttaatgttggtcagATGAGCACATACTCCTCAATGGATGGAATTCTTTATTGCAAGACACATTTTGAACAGCTTTTCAAGGAATCTGGAAATTTCAGCAAGAACTTTG------
upper sequence: AT3G61230.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G08020.1 (Glycine max), 3'ss of exon 1
---------------------gtatctatctatcttccttttcctccattgttccctcatgaaaaaaaaaacacaaagagaacatctttcttctccttttcagATATGTAACTACTCATCCATGGATGGAGTTTTGTATTGCAAGACCCATTTTGAACAGCTCTTCAAAGAATCTGGAAATTTCAGCAAGAATTTCCAAACAG
|| | | || || | | | | || | ||| | | || | | || | | | |||||| || | ||||| || ||||||||| || | ||||||||||| |||||||||||||| ||||| |||||||| |||||||||||||| |||
gattaaattcttttcaatacaaaataagttaagattaaattcctttaaatattgttcct--aaatcgagggtgccaatgatata-ctacttaatgttggtcagATGTGCACATACTCCTCAATGGATGGAATTCTTTATTGCAAGACACATTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTCG------
upper sequence: AT3G61230.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G46460.1 (Glycine max), 3'ss of exon 1
-------------------------gtatctatctatcttccttttcctccattgttccctcatgaaaaaaaaaacacaaagagaacatctttcttctccttttcagATATGTAACTACTCATCCATGGATGGAGTTTTGTATTGCAAGACCCATTTTGAACAGCTCTTCAAAGAATCTGGAAATTTCAGCAAGAATTTCCAAACAG
| | | || | | | |||||| | ||| | || | || || || | | ||||| | |||||| || |||||||| || | ||||||||| | || ||||||||||| ||||| |||||||| |||||||||||||| || |||||||
gtattttgatatggtttgattcaaggaaagaagaaatatatgtagtttaaaattgtttct-------aaatttggtgctaatggtgcaatgttattttggtcaccagATGAACACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
upper sequence: AT3G61230.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G39740.1 (Glycine max), 3'ss of exon 1
--------------gtatctatctatcttccttttcctccattgttccctcatgaaaaaaaaaacacaaagag---aacat-ctttcttctccttttcagATATGTAACTACTCATCCATGGATGGAGTTTTGTATTGCAAGACCCATTTTGAACAGCTCTTCAAAGAATCTGGAAATTTCAGCAAGAATTTCCAAACAG
|| | | ||| || | | | ||| | | || | || || ||| || | || |||||| | | |||||| || |||||||| || | ||||||||| | || |||||||| || ||||| |||||||| |||||||||||||| || |||||||
tttgatatggtttgatacaatgaaagaagacatttatgtagtttaaacttgttccaaactttggcgctaatggtgcaatatattttattttggttatcagATGAGCACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAACTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
upper sequence: AT3G61230.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0046g03370.t01 (Vitis vinifera), 3'ss of exon 1
--------------------gtatctatctatcttccttttcctccattgttccctcatgaaaaaaaaaa----cacaaa-----gaga----acatctttcttctccttttcagATATGTAACTACTCATCCATGGATGGAGTTTTGTATTGCAAGACCCATTTTGAACAGCTCTTCAAAGAATCTGGAAATTTCAGCAAGAATTTCCAAACAG
| | || | || |||| | | | | ||||| || | | ||| |||| ||| | || | |||| ||||| | |||||||||||||||||||| || | || ||||| | |||||||| ||||| ||||| || ||||| ||||||||||||||||| ||||||
gtatgtttcttctaagcctatttttcccctgtttttttttttttttggtaaatttttacgaaaatcaatatctacgtaaatttatgagatataacaagtgggttttactttgcagATGAGCAACTACTCATCCATGGATGGGGTCCTCTACTGCAAACCTCATTTTGAGCAGCTGTTCAAGGAGTCTGGCAATTTCAGCAAGAATTTTCAAACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttccctcatgaaaaaaaaaacacaaagagaacatctttcttctccttttcagATATGTAACTACTCATCCATGGATGGAGTTTTGTATTGCAAGACCCATTTTGAACAGCTCTTCAAAGAATCTGGAAATTTCAGCAAGAATTTCCAAACAG
catctttcttctcctt CT-rich tract
aaaaaaaaaacacaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctatctatcttccttttcctccattgttccctcatgaaaaaaaaaacacaaagagaacatctttcttctccttttcagATATGTAACTACTCATCCATGGATGGAGTTTTGTATTGCAAGACCCATTTTGAACAGCTCTTCAAAGAATCTGGAAATTTCAGCAAGAATTTCCAAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA