Sequence
atgc intronic sequence ATGC exonic sequence...agactctaaaacttagtctatattttaaccattagattgttagttacaaaagcaacttgtattggataatgttgaaatttgatttcatttatatgagtagGAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGAAGAAGAACATCTTCAAGTTGTCTCAAGGTGAATATGTTGCTGTTGAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G49430.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G49430.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os11g35400.2 (Oryza sativa), 3'ss of exon 15
----agactctaaaacttagtct-atattttaaccattagattgttagttacaaaagcaacttgtattggataatgttgaaatttgatttcatttatatgagtagGAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGAAGAAGAACATCTTCAAGTTGTCTCAAGGTGAATATGTTGCTGTTGAAAA
|| | | | || ||| | | ||| | | || ||| | || |||| | || | | ||| || | || ||| | ||| ||||| || || |||||| ||| || |||||||||||||||| || ||||||||||| |||||| |||| ||||| || ||||| || || ||
gtaaagtcatttaccctcagtttcacgccttactgaatgatctgacagt---ggagataaattgtctcaaatta----gcaatc--atcttatgtat----gaagGTGATATCGGTGAGTGGCAACCAGACGGCACAATGAAGATCATCGACAGAAAGAAGAACATTTTCAAGCTGTCCCAAGGGGAGTATGTAGCAGTGGAGGT
upper sequence: AT1G49430.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G104847_T01 (Zea mays), 3'ss of exon 15
------agactctaaaacttagtctatattttaaccattagattgttagttacaaaagcaacttgta------ttggataatgt-tgaaatttgatttcatt-tatatgagtagGAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGAAGAAGAACATCTTCAAGTTGTCTCAAGGTGAATATGTTGCTGTTGAAAA
| |||| | | | | || | | || | | | || || ||| || || || ||| ||| ||| || | ||| ||||| || || |||||| |||| | |||||||||||||| || |||||||||||||||||| |||| || || || ||||| || |||||
gtgaaagaataaaaaaaatcatttctcacttcttttaatttgcacctaactgaaggatcagtcagtgaagcagctggtcgattcgtggaacttgtcatcaccctatgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAAAGAAGAACATCTTCAAGCTGTCCCAGGGGGAGTATGTGGCAGTTGAGGT
upper sequence: AT1G49430.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA07G20860.1 (Glycine max), 3'ss of exon 15
agactctaaaacttagtctatattttaaccattagattgt--tagttacaaaagcaacttgtattggataatgtt---gaaatttgatttcatttatatgagta--gGAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGAAGAAGAACATCTTCAAGTTGTCTCAAGGTGAATATGTTGCTGTTGAAAA
| || | ||| |||| | | | |||||| || ||| | |||| ||| | | ||| || | | || || |||||||||||||||||| | ||||| | ||||| || || |||||||||||||| ||||| || ||||| ||||| |||||| ||||||| || ||
-----------------------gtaaatc--taggttgtcctggattcaaaagtcacagtgatttgttaatccacaaaaaactcacatacatataaaccattacagGTGATATTGGAGAATGGCAATCAAATGGAGCCATGAAAATTATTGATAGGAAGAAGAATATCTTTAAATTGTCCCAAGGAGAATATATTGCTGTGGAGAA
upper sequence: AT1G49430.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA12G05140.1 (Glycine max), 3'ss of exon 15
-agactctaaaacttagtctatattttaaccattagatt-gttagttacaaaagcaac-ttgtattggataatgttgaaatttgatttcatttatatgagtagGAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGAAGAAGAACATCTTCAAGTTGTCTCAAGGTGAATATGTTGCTGTTGAAAA
| | | || | || | || | || | |||| | ||| | | || | |||| || | |||| | || | ||| || |||||||||||||| | ||||| | ||||| || || ||||| || ||||| ||||| |||||||||||||| |||||||||||||| || ||
ggaatcccagtgaagagggcacataggag--atcaagttagggagttttgtcatgaacatcaaaatgcagcgtgttttaaaataatttgaaaatcatta-cagGTGACATTGGAGAATGGCAGCCAAATGGAGCCATGAAAATTATTGATAGAAAAAAGAATATCTTTAAGTTGTCTCAAGGAGAATATGTTGCTGTGGAGAA
upper sequence: AT1G49430.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA11G13050.1 (Glycine max), 3'ss of exon 15
agactctaaaacttagtct--atattttaaccat-tagattgtt--agttacaaaagcaacttgtattggataatgttgaaatttgatttcatttatatgagtagGAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGAAGAAGAACATCTTCAAGTTGTCTCAAGGTGAATATGTTGCTGTTGAAAA
| | || || | || | ||| ||||| || |||| || | | || | ||| | |||| | || | ||| || |||||||||||||| | ||||| | ||||| || || ||||| || ||||| ||||| |||||||||||||| ||||||||||| || || ||
----tttcggtttttgtttgaatgcatagtgcatatagatcattgaagttgttaatttgcccctaaatgcagtgcgttttggaataatttgaaaatcatta-cagGTGACATTGGAGAATGGCAGCCAAATGGAGCCATGAAAATTATTGATAGAAAAAAGAATATCTTTAAGTTGTCTCAAGGAGAATATGTTGCCGTGGAGAA
upper sequence: AT1G49430.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA20G01060.1 (Glycine max), 3'ss of exon 15
agactctaaaacttagtctatattttaaccattagattgttagttacaaaagcaacttgtattggataatgttgaaatttgatttcatttatatga--gtagGAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGAAGAAGAACATCTTCAAGTTGTCTCAAGGTGAATATGTTGCTGTTGAAAA
| | | | || | | |||| | ||| | || | ||||| || | ||||| | || || | | | ||| || ||||||||||||||| | |||| | ||||| || || ||| |||||||||| ||||| || ||||||||||| |||||| ||||||| || ||
-----------gtaaaaccaggttgtc----ctggattcaaaattaacatagtgatttgta---aatcaacacaaaattcacatacaggtaaaccattgcagGTGACATTGGAGAATGGCAATCAAATGGGGCCATGAAAATTATTGATCGGAAGAAGAATATCTTTAAATTGTCTCAAGGAGAATATATTGCTGTGGAGAA
upper sequence: AT1G49430.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv03s0063g01880.t01 (Vitis vinifera), 3'ss of exon 15
agactctaaaacttagtctatattt--taaccatta--gattgttagttacaaaagcaacttgtat-tggataatgttgaaatttgatttcatttatatgagtagGAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGAAGAAGAACATCTTCAAGTTGTCTCAAGGTGAATATGTTGCTGTTGAAAA
||| || || | ||| ||| || || || ||| | | |||| | | | | | | || | | | ||| | ||| ||||||||||||||||| ||||| ||||||| || || || ||||| ||||||||||| ||| | |||||||| |||||||||||||| || ||
-----ttaatttttggttttgctttcctaatttttctcacttttttgttttgagatttacttacaggtatttgagaataatatctacaatattggatacttgcagGTGATATTGGAGAATGGCAGCCCAATGGAGCAATGAAAATTATTGACAGGAAAAAGAACATCTTTAAGCTCTCTCAAGGGGAATATGTTGCTGTGGAGAA
upper sequence: AT1G49430.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: PP1S113_124V6.1 (Physcomitrella patens), 3'ss of exon 15
-agactctaaaacttagtctatattttaaccatt--agattgttagttacaaaagcaacttgtattggataatgttgaaatttgatttcatttatatga--gtagGAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGAAGAAGAACATCTTCAAGTTGTCTCAAGGTGAATATGTTGCTGTTGAAAA
||||| || || ||| ||| | ||| || | || || | | | | | ||| |||| | |||||| ||| | | ||| ||| |||||||||||||||| ||||| | |||||||| ||||| |||||||| ||||| || || ||||| ||||| ||||| ||||| || || ||
ccccctctagaagtttttct---ctttgagtatttcaggtaacaagctagatccgtagcgtagtgctgatgatgt--agtgctgattttgaccatagtactgcagGTGATGTTGGAGAATGGCAAGAGGATGGTGCCATGAAGATTATCGACAGGAAGAAAAACATTTTTAAATTGTCACAAGGAGAATACGTTGCAGTCGAGAA
upper sequence: AT1G49430.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: PP1S218_19V6.1 (Physcomitrella patens), 3'ss of exon 16
------------------------------------------------agactctaaaacttagtctatattttaaccattagattg--ttagttacaaaagcaacttg----tattggataatgttgaaatt-tgatttcatttatatga--gtagGAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGAAGAAGAACATCTTCAAGTTGTCTCAAGGTGAATATGTTGCTGTTGAAAA
|| | || || | | || || | | | || ||| | | || || | || ||| || | ||| ||||| || || | | ||| ||||| || || ||| | |||||||||| ||||||||||||| |||||||||||||||||||||||||| || |||||||| |||||||| || ||
gtaatgtcttctctttaattgacgttttctttttaaataatttggatcttgctttttccctcagagagtgtctttttgtttcgttggaattgtttatattaacactgtggaactgctgcatatggtctacattctgattctcttcgtaaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAA
upper sequence: AT1G49430.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: PP1S47_161V6.1 (Physcomitrella patens), 3'ss of exon 15
-agactctaaaacttagtctatattttaaccattag--attgttagttacaaaagcaacttgtattggataatgttgaaatttgatttcatttatatgagtagGAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGAAGAAGAACATCTTCAAGTTGTCTCAAGGTGAATATGTTGCTGTTGAAAA
|| || ||| ||| || || |||| || || | | | | || | || || || || | | || | | | | ||| ||||||||||| |||||| ||||||| | ||||||| || ||| | |||||||||||||||||| | |||||||| ||||| ||||| || |||||
caggggctgtt-cttgaaatatgttgaaaggattatccatctttgggtcgatgaataagtca-atgatgacatagacaagttctttgtgatgtgtgt-atcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAAMapped 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|124998158|gb|EL070427.1|EL070427EST: TCCTAATCGATGGATGGTTCCACACAG GAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGNTCATCGATAGGA
genomic: TCCTAATCGATGGATGGTTCCACACAGgtattgttgt ... atatgagtagGAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGA
EST:
gi|164225331|gb|EL993620.1|EL993620EST: CTAACTGATCAAGTCCTAATCGATGGATGGTTCCACACAG GAGATATTGGAGAATGGC
genomic: CTAACTGATCAAGTCCTAATCGATGGATGGTTCCACACAGgtattgttgt ... atatgagtagGAGATATTGGAGAATGGC
EST:
gi|116420467|gb|EG463059.1|EG463059EST: AAGACAAGATCTAACTGATCAAGTCCTAATCGATGGATGGTTCCACACAG GAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGA
genomic: AAGACAAGATCTAACTGATCAAGTCCTAATCGATGGATGGTTCCACACAGgtattgttgt ... atatgagtagGAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaaaagcaacttgtattggataatgttgaaatttgatttcatttatatgagtagGAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGAAGAAGAACATCTTCAAGTTGTCTCAAGGTGAATATGTTGCTGTTGAAAA
atttgat putative branch site (score: 5)
ataatgttgaaatttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agactctaaaacttagtctatattttaaccattagattgttagttacaaaagcaacttgtattggataatgttgaaatttgatttcatttatatgagtagGAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGAAGAAGAACATCTTCAAGTTGTCTCAAGGTGAATATGTTGCTGTTGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - -ctaaaac
- - - - - - - - - - - - - - - - - - - - - - - caaaagc