Sequence
atgc intronic sequence ATGC exonic sequencegttgtttttttattttataatattaaactttgtttgactttcgttagtaatgttacatatacttacttaaaaggttatgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G37750.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G05170.1 (Glycine max), 3'ss of exon 4
------gttgtttttttattt-tataatattaaactttgtttgactttcgttagtaa-----tgttacatatacttacttaaaaggtta--tgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
||| ||| ||| | || || | | ||| | | || ||| ||||| | | | | | | || | | || ||||||||||||||||| |||||||| ||| | ||||| ||||||| |||||||||||| || | ||| |||||||||||||
gttttgaagctttctttgtttgtgtaccttttactctaatttccaatctgataataaattcttgttaattgaattctggtgattgttttcttttcctttagGCATAGATGGACTGGTAGGTATGAAGCGCATTTGTGGGATAATAGTTGCAAGAAGGAAGGGCAGACTAGGAAAGGAAGACAAG
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 1
--------------gttgtttttttatttta---taatattaa-actttgtttgactttcgttagtaatgttacatatacttacttaaaaggttatgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
||| || || | | |||| | || | | ||||||| | ||| | | || | | | || | | || || ||| ||||| ||||| ||||||||||||||||||||||||||||||||||| || | |||||| || || || | || |||||||| ||||
tccttgctcaagaagttaagggttcatgtaagattaatgtcaacaacatatttgactgt--ttatt--ttttgctttgatttccaaagaatatt-tgttcaacagGCATAGGTGGACTGGTAGATATGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G05080.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------------gttgtttttttattttataatattaaactttgtttgac---tttcgttagtaatgttacatatacttacttaaaaggttatgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
| ||||| || | || || ||| ||| | | ||||| | ||| || || ||| | | | | || ||||||||||||||||| |||||||| ||| | ||||| ||||||| |||||||||||| || | ||| |||||| ||||||
gttagttaatagttttgaaactttctttgtttgtgtaacttttaccgaaatttccaatctggaaataaattggttttctttgtctagtcaatcctgttttttttaatagatgtcgttgattgagttgtggattattgctt------tcttttccattagGCATAGATGGACTGGTAGGTATGAAGCGCATTTGTGGGATAATAGTTGCAAGAAGGAAGGGCAAACTAGGAAAGGACGACAAG
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G10130.1 (Glycine max), 3'ss of exon 5
-------------gttgtttttttattttataatattaaact--ttgtttgactttcgttagtaatgttacatatacttacttaaaaggttatgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
||| ||||| | |||| || | | ||| || ||| ||| || || | ||| | || ||| | ||| |||||||||||||||||||||||||| ||| | ||||| || |||| |||||||||||| || | || |||||| ||||||
attcatggtggttgttactttttgagtttaacttaatgtgttgtttgctttgttttttgagtaaattttgtggtgacattcttggttg-ttgtgt-atgcagGCATAGATGGACTGGTAGATATGAAGCGCATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACCAGGAAAGGACGACAAG
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA0041S00200.1 (Glycine max), 3'ss of exon 5
----------------gttgtttttttattttataatattaaactttgtttgactttcgttagtaa-tgttacatatacttacttaaaaggttatgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
| |||||| ||| | | |||| | || | ||| | ||||| | || || | ||| |||| ||| | ||| |||||||||||||||||||||||||| ||| | ||||| || |||| |||||||||||| || | || |||||| ||||||
tatttagtcaaattcatggggatttttactttttgagtttaacttatggt--gtttttttaagtaaattttgtggtgacattcttggt-ggttgtgt-atgcagGCATAGATGGACTGGTAGATATGAAGCACATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACAAGGAAAGGACGACAAG
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G22970.1 (Glycine max), 3'ss of exon 4
------------gttgtttttttattttataatattaaactttgtttgactttcgttagtaatgttacatatacttacttaaaaggt-tatgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
|| | | |||| | | | |||| ||| || | ||| | | | | |||| ||| | |||| | ||| ||||| |||||||| ||||||||||||||||| |||||||| || | |||||| || || || || || |||||||||||||
tgagcaatgagcattctcaactcatttaactgttcatcttcctttttgtgttttgtgttttatgatttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 3
--------gttgtttttttattttataatattaa--actttgtttgactttcgttagtaatgttacatatacttact--taaaaggt-tatgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
| | | || | | || | || | |||| ||| || | ||| | | | ||| | |||| ||| | |||| | ||| ||||| |||||||| ||||||||||||||||| |||||||| || | |||||| || || || || || |||||||||||||
gcaatgagcatcctccaacacatttaactgttcatcaccctttttgtgttttgtgttttatgatttttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G04910.1 (Glycine max), 3'ss of exon 3
---gttgtttttttatt-----ttataatattaaactt---tgtttgacttt-cgttagtaatgttaca-tatacttacttaaaaggttatgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
|||| | || || || | | | || ||||| ||| || | ||||| | || || || | | | ||| | ||| ||||| |||||||||||||| |||||||||||||||||||| || | |||||| || || || | || |||||||| ||||
ttaagtgttcatgtaagagcaattccaacaacatatttgactgtttacttttattttttttatgttttgctttaatttctaaggaatgtttgttcatcagGCATAGGTGGACTGGTAGATACGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 2
--------------gttgtttttttattttataatattaaactttgtttgactttcgttagtaatgttacatatacttacttaaaaggttatgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
||||| |||| | | || | | || | ||| || | | | || |||||| | ||| ||||||||||| ||||||||||||||||||||||||||||| |||| |||||| ||||| || || || |||||||| ||||
gtgtttttttccctcatgtttcccccttttgccttccttgttttcctatcacatct-ttaccttctttttttttttctttttcctgttttatgtctatcagGCATAGATGGACAGGTAGATATGAAGCTCATCTATGGGACAACAGTTGCAAGAAAGAAGGGCAAAGCAGGAAAGGAAGGCAAG
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------------------------------------------------------------------gttgtttttttattttataatattaaactttgtttgactttc--gttagtaatgttacatat---acttacttaaaaggttatgtgaaa---------cagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
|||| | | |||| | ||||| | | | | | |||| | | | ||| || | | || | | | ||| || ||| |||||||||||||||||||||||||| ||||| ||||| ||||||| ||||||||| || || | ||| |||||||||||||
gttagttcatattcttttccttcatctttggtcttatctataatgttttttgaattgagtttgttttctagtttatttgaggtctccctgcaggtgtattgtatcactgttttctc-tattatattgtcctcgccttttctgctggaaatattgtaggtttggttttccaagtaaacattgtcaatttatttccccagGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAAGAAGGAGGGGCAGACTAGGAAAGGAAGACAAGMapped 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|124934684|gb|EL011735.1|EL011735EST: CTTTTGGACAACGAACTTCTCAATACCGAGGCGTTACAAG ACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAA
genomic: CTTTTGGACAACGAACTTCTCAATACCGAGGCGTTACAAGgttgtttttt ... tgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgactttcgttagtaatgttacatatacttacttaaaaggttatgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
tacttac putative branch site (score: 1)
atatacttacttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgtttttttattttataatattaaactttgtttgactttcgttagtaatgttacatatacttacttaaaaggttatgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA