Sequence
atgc intronic sequence ATGC exonic sequencegtaaagaaatcagcttaaacactaatagttaacgtcaatactatataatgattttgtctctgaacatagCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55810.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 11
------------------------gtaaagaaatcagcttaaacactaatagtta-----acgtcaatactatataatgattttgtctctgaacat--agCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG
|| || ||| | | | ||| | || || | | || | | | | || | | | | || ||||||||||||||||| || | | |||||||| ||||| || ||||||||||||||||| ||||| |||||||| |||||||| |||||
attcaatttcttgttaaagattctgttaataaagctcttcatacatccttgagtataaatacataactattgtcaattatttcttacaattgctttccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGTAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGAGAAGGAGACAATGGCAAACAG
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
-----------------------------gtaaagaaatcagcttaaacactaatagttaacgtcaatactatat-aatgattttgtct---ctgaacatagCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG
|||||| | || | |||| | | || | || ||||| | ||| ||||| | | || ||||||||||||||||| || | | |||||||||||||| || ||||||||||||||||| ||||| || ||||| |||||||| |||||
ggattcattccttgtcaagtatcttgttagtaaagca--catcataaatttttgaatagaaaggcataactatgttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 12
-----------------------------gtaaagaaatcagcttaaacactaatagttaacgtcaatactatataatgattt--tgtctctgaacat-agCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG
| | | || | | | | ||| || | || | |||||||| | ||| || || || || |||||||| || | |||||||||| ||||| || || |||||||||||||| |||||| | ||||| |||||||| ||||||
ttcatgcactagaattcaattcatcacaagaacatgtatgatcccccctatccttgaataaagtgtactctgca-aatgatttgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 10
-----------------------gtaaagaaatcagcttaaacactaatagtta--acgtcaat--actatataa-tgattt--tgtctctgaacat-agCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG
| | ||| || | || | || | || || || ||| || || |||||| | ||| || || || ||||||||||| || || | |||||||| ||||| || || |||||||||||||| |||||| | ||||| |||||||| ||||||
aacatgcacaattgacccctcatgcactagaattcaattcatcagtcatcacaagaacatctatgtactctacaaatgatttgctacaactggtttccagTGGCGAAAGTATGGAGAATGCACTACGTGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGTGACAATGGACAACAG
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 11
----------------------------gtaaa---gaaatcagcttaaacactaatagttaacgtcaatactatataatgattttgtctctgaacatagCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG
|| | |||| || ||| || | | || | |||| | ||| | || || ||||||||||| || ||||| |||||||||||||||| ||||| |||||||| ||||| |||||||||||||| |||||||||||||||
ttcttctttcctaattactcggtttaatgtggacctatgatcactgcaattttatataaatagaatttgtccttaaatttgatatgcaatctaatttcagTGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAG
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 11
-----------------------------gtaaagaaatca--gcttaaacactaata-gttaacgtcaatactatataatgattttgtctctgaacatagCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG-
|| | || | | | ||| | | | || || ||| | || | ||| | | | | || | || || |||||||||||||| ||| | ||||||||||| ||||| ||||| |||||||| ||| | ||||| |||||||| ||||||||||| |||
ccttaagaaaccttgtgtgtatctttgcagtctataatttattgtttagaaattcatttactattatcataattaaaaaattaatatatg-ctaatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGG
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 11
-----------------------------gtaaagaaatcagcttaaacactaatagttaacgtcaatactatataatgattttgtctctgaacat---agCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG
|| | || | | | || | | || || | | || |||| |||| | | || ||| || || |||||||||||||| ||| | ||||||||||| ||||| || || |||||||| ||| | ||||| |||||||| ||||||||||| |||
ccctaagaaaccttgtgtgtctctctgcagtttataatttattgttaagaaattcattttctgttatcataat-taataatttaatatatgctcatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAG
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 8
-----------------------------------------------------------------gtaaa---gaaatcagcttaaacactaatagttaacgtcaatactatataatgattttgtctctgaacatagCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG
|| || |||| || | ||| | | | || | |||| | ||| | || || ||||||||||| || ||| | |||||||||||||||| ||||| |||||||| |||||
ttgaaaatattatccaacctatattctaagaaactagttcttctttcctaattactcagtttgatgtgaacctatgatcactgcaattttttataaacagAATTTGTCCTTAAATTTGATATGCAATCTAATTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCT-------------------------------
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 11
----------------------------gtaaagaaatcagcttaaacactaatagttaacgtcaatactatat-aatgattttgtct--ctgaacatagCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG
| || | | || | || || | | | || || || ||| |||| || ||||||||||||||||| ||| | ||||||| |||||||| |||||||||||||||||||| || ||||| ||||| || || ||||| |||
aaaggaaaaagaagtgcaaaaagcatattcctggttatggacccattttctctttgtcttttgcattttggtttgaaccatcttctcttactgatgccagTGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAG
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S83_234V6.4 (Physcomitrella patens), 3'ss of exon 11
-------------------------------------------------------------gtaaagaaatcagcttaaacactaatagttaacgtcaatactatataatgattttgtctctgaacatagCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG
| | | | || | | | | | | || || | ||| || | || || |||||| ||||| |||||||| || || | || ||||||||||||||||| ||||| |||||| |||| ||| | ||||| || ||||| ||||||
gtattattcctcattacgagttaccaccagtgattatgtgaattggctgtgtggaactggtatgtggggctgatctaatgtcattacaagtga-gttgctaat-tattattgtcgggttctgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGATTGGAAAGATTTTGATACATCGCGAAGGAGATAATGGGCAACAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86074649|gb|DR370406.1|DR370406EST: TCGGGTGTGGACTTCTGTAAGAAACTGTGTGGTGTCTCAGTTATCAGAAG CGGTGAGAGTATGGAGWACGCTCTTAGAGCATGCTGCAAAGGCATCAAAAT
genomic: TCGGGTGTGGACTTCTGTAAGAAACTGTGTGGTGTCTCAGTTATCAGAAGgtaaagaaat ... ctgaacatagCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAAT
EST:
gi|124897070|gb|EH973284.1|EH973284EST: TCGGGTGTGGACTTCTGTAAGAAACTGTGTGGTGTCTCAGTTATCAGAAG CGGTGAGAGTATGGAGAACGCTC
genomic: TCGGGTGTGGACTTCTGTAAGAAACTGTGTGGTGTCTCAGTTATCAGAAGgtaaagaaat ... ctgaacatagCGGTGAGAGTATGGAGAACGCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaacactaatagttaacgtcaatactatataatgattttgtctctgaacatagCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG
ttttgtctct CT-rich tract
tcaatactatataatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagaaatcagcttaaacactaatagttaacgtcaatactatataatgattttgtctctgaacatagCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA