Sequence
atgc intronic sequence ATGC exonic sequencegtgcactcattactcattttcttgttagatcttctatgatcatattatatcaacaatttatctatgtgttgatggcagATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01780.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os10g35930.1 (Oryza sativa), 3'ss of exon 1
------------------------------------gtgcactca-ttactcattttcttgttagatcttctatgatcatattata-tcaacaatttatcta---tgtgttgatggcagATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
| ||| || | || |||| | ||| || | || |||| || ||| | | || | ||| | | |||||| ||| |||||| |||||||| || ||| | ||||||||||| ||||||||||| || ||||||||| | |||| |||| || ||||| | |||
gtatgcactcttcttggtgtctgcactccttgatgtgaatgatcagttttttatgctcttcat-gatgttaaaatattatatgttactcatgagctgatgtgaattgttctatttccagATGTGCAGCTATTCGTCCATGGATGGGGTTCTTTACTGCAAGACCCATTTTGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAG
upper sequence: AT1G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os04g45010.1 (Oryza sativa), 3'ss of exon 1
-----------------------------------------gtgcactcattactcattttcttgttagatcttctatgatcatattatatcaacaatttatctatgtgttgatggcagATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
| || | ||||| | || | | | | | | | ||| | | |||| ||| ||||| ||| ||| || ||||||||||| || | ||||||||||| || |||||||| ||||||||||| | || | ||| ||| || || ||||
gtaacgctcaacaacaccagattttctttttccctgtgggaaatcgatcgtaactcacatggttaattgtgatcgcgcgctgcagaggca-cgttgattaacttgtgtgg-gatcttagATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTTGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAG
upper sequence: AT1G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G153268_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------gtgcactcattactcattttcttgttagatcttctatgatcat--attatatc---aacaatttatctatgtgttgatggcagATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
|||| || | || || | | | || || | | | | || || | || | | ||||||| ||| ||| |||||||||||||| || ||||||||||||| || || ||||| ||||||||||| | || | ||| ||| ||||| ||||
gtacgtgcatatgtcctgatgtccatggcttagaaaaacgatcgatccagtttattatcatccgatctctgcatgcaaaaa-cacaaaaacaagagctttctgacgacgatgcagcaaaccgagaatgatgcgttaattggccgcctgcagATGTGCAGCTACTCCTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTCGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG
upper sequence: AT1G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G134752_T02 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------------gtgcactcatt---actcattttcttgttagatcttctatga--tcatattatatcaacaatttatctatgtgttgatggc------agATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
||| |||| | || ||| | | || | |||||||| || | ||| | || ||| | |||| |||| ||| || ||||||||||| ||| ||||||||||||| || ||||| || ||||||||||| | || || ||| ||| || || |||
gtacgcatgccgcatggcccccctcaagccctcaacactcttactcctcacgcgcatttgccttcctgtgaatcctgtgatacgcattcatcccgatagatgacaatgtagggaataatacgggctcatattaattcttttctgcatccgtcggtcgatctcctctctagATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTTGAACAGCTCTTCAAGGAGACGGGGAACTTCTCCAAGAAATTCCAAG---
upper sequence: AT1G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G024887_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------gtgcactcattactcattttcttgttagatcttctatgatcatattatatcaacaatttatctatgtgttgatggcagATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
| | | | | |||| | | | ||| | | || ||| ||| ||| | | ||||||| ||| ||| || ||||||||||| || ||||||||||||| || || ||||| ||||||||||| | || | ||| ||| ||||| ||||
gtacgtcgtgccgtacgtgcgtgcatccaaatgccatgtctgcatgccatgggaaagaagaaaaaaacggccgagttaaagagtttctgacgctgcaa-ataaaccgtttg---atg-gccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTCGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG
upper sequence: AT1G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G170034_T02 (Zea mays), 3'ss of exon 1
----------------------------------------------------------------------------------------------------------gtgcactcattactcattttcttgttagatcttc-tatgatcatattatatcaacaatttatct----atgtgttgatggcagATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
| | || | | || ||| | |||| | | | ||| | ||| || || | ||| || ||||| |||| ||| || ||||||||||| || ||||||||||||| || ||||| || ||||||||||| | || | ||| || |||||||||
gtatgcatgcgtggcctgagctcaactccgcatgcgcattcgccctgcttgcgatgtgtgcggcaatgcgctaatgctcatttgcatcgaaagaaacgaagctttgtttgattcggttcagatcatctcgacagatgaacatgtagaaatacggtctcattttttcatttctgcatgcgtctcctccagATTAGCAGCTACTCTTCCATGGACGGCGTCCTGTACTGCAAGACGCACTTTGAACAGCTCTTCAAGGAGACAGGGACCTTCTCAAAGAACTTTCAAGGTA
upper sequence: AT1G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G170034_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------------------------------------------------------------------gtgcactcattactcattttcttgttagatcttc-tatgatcatattatatcaacaatttatct----atgtgttgatggcagATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
| | || | | || ||| | |||| | | | ||| | ||| || || | ||| || ||||| |||| ||| || ||||||||||| || ||||||||||||| || ||||| || ||||||||||| | || | ||| || |||||||||
gtatgcatgcgtggcctgagctcaactccgcatgcgcattcgccctgcttgcgatgtgtgcggcaatgcgctaatgctcatttgcatcgaaagaaacgaagctttgtttgattcggttcagatcatctcgacagatgaacatgtagaaatacggtctcattttttcatttctgcatgcgtctcctccagATTAGCAGCTACTCTTCCATGGACGGCGTCCTGTACTGCAAGACGCACTTTGAACAGCTCTTCAAGGAGACAGGGACCTTCTCAAAGAACTTTCAAG---
upper sequence: AT1G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G39740.1 (Glycine max), 3'ss of exon 1
--------------gtgcactcatt--actcattt-tcttgttagatcttctatgatcatattatatcaa-----caatttatctatgtgttgatggcagATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
| || | | | ||||| | | ||| | ||| | | | | || |||| ||| | | | | | |||||||||| ||| ||||| ||||| || || | || |||||| | || ||||| ||||| |||||||||||||||||||||||||| ||||||||| |||
tttgatatggtttgatacaatgaaagaagacatttatgtagtttaaacttgttccaaactttggcgctaatggtgcaatatattttattttggttatcagATGAGCACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAACTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
upper sequence: AT1G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G01590.1 (Glycine max), 3'ss of exon 1
---------------------gtgcactcattactcattttcttgttagatc-ttctatgatcatattatatcaacaatttatctatgtgttgatgg-cagATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
| || ||| || | || | | || ||| || | ||| || || ||| | || ||| |||||||||| || ||||| ||||| ||| || | || |||||||| |||||||| || || |||||||||||||| ||||||||||| ||||||
gaagtaaattgatatgatactattcattcaaataaaatgtcattttaacattgttcctaaattcgggggtgccaatgatata-ctacttaatgttggtcagATGAGCACATACTCCTCAATGGATGGAATTCTTTATTGCAAGACACATTTTGAACAGCTTTTCAAGGAATCTGGAAATTTCAGCAAGAACTTTG------
upper sequence: AT1G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G08020.1 (Glycine max), 3'ss of exon 1
----------------------gtgcactcattactcattttcttgttagatcttctatgatcatattatatcaacaatttatctatgtgttgatgg-cagATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
| | | | | | || ||| | || | | | | | ||| || || ||| | || ||| |||||| ||| || ||||| ||||| ||| || | || |||||||| |||||||| || || |||||||||||||||||||||||||| |||||
gattaaattcttttcaatacaaaataagttaagattaaattcctttaaatattgttcctaaatcgagggtgccaatgatata-ctacttaatgttggtcagATGTGCACATACTCCTCAATGGATGGAATTCTTTATTGCAAGACACATTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTCG------
upper sequence: AT1G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G46460.1 (Glycine max), 3'ss of exon 1
-----------------------gtgcactcattactcattttcttgttagatcttctatgatcatattatatcaacaatttatctatgtgttgatggc-agATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
| | | | | | | | | | || | | | | || | | || | | | | ||| | | |||||| || ||| ||||| ||||| || || | || |||||| | || ||||| || || |||||||||||||||||||||||||| ||||||||| |||
gtattttgatatggtttgattcaaggaaagaagaaatatatgtagtttaaaattgtttctaa--atttggtgctaatggtgcaatgttattttggtcaccagATGAACACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
upper sequence: AT1G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0046g03370.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------gtgcactcattactcattttcttgttagatctt--ctatgatca-tat-----tatatcaacaatttatc-----tatgtgttgatg-gcagATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
| | || || | |||| ||| || || || | | |||| ||| || || | | ||| | || || | ||||||||||||||| || |||||||| || || | |||||||| ||||||||||||| || |||||||| ||||||||||||||||| || |||||| ||
gtatgtttcttctaagcctatttttcccctgtttttttttttttttggtaaatttttacgaaaatcaatatctacgtaaatttatgagatataacaagtgggttttactttgcagATGAGCAACTACTCATCCATGGATGGGGTCCTCTACTGCAAACCTCATTTTGAGCAGCTGTTCAAGGAGTCTGGCAATTTCAGCAAGAATTTTCAAACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttagatcttctatgatcatattatatcaacaatttatctatgtgttgatggcagATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
tgttgat putative branch site (score: 4)
tatgatcatattatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcactcattactcattttcttgttagatcttctatgatcatattatatcaacaatttatctatgtgttgatggcagATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA