Sequence
atgc intronic sequence ATGC exonic sequencetacaactataataacactttgttttgtttttcatagtatggagcgaatgatttcaagtatgttatgattattaggttaattatacactttatctttgctgacatccttctttctgcttgtaggCTATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGCGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAAGAAGA
Basic information
species | Glycine max |
transcript | GLYMA18G44630.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G44630.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g60700.2 (Oryza sativa), 3'ss of exon 3
--tacaactataataacactttgttttgtttttcatagtatggagcgaatgatttcaagta-tgttatgattattaggttaat---tatacactttatcttt---gctgacatccttct----ttctgcttgtaggCTATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGCGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAAGAAGA
||| || | | || ||||| || | || | | | |||| | || | ||| | | |||| || | | || || | || || || | | | || | || |||| ||||| ||||| |||||||| | ||||| || |||||||||||||||| |||||||| ||||||||||| ||||||||| | | |||| || |
gttactgcttctaaactttttctttttgacattaccaataagtgaatatttattttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgttattttttttacagGCCATGTACAATGACTTCTCAACCTCAAACATCCAAATTGACAAAGATTTCACTGCAAAGCTATCAGGATATGGATGTGTTGGATTCAATACCGAGGAGG-
upper sequence: GLYMA18G44630.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G828466_T01 (Zea mays), 3'ss of exon 1
-------tacaactataataacactttgttttgtttttcatagtatg-gagcgaatgatttcaagtatgttat--gattat-taggttaattataca----ctttatctttgctgacatccttctttctgcttgt-----aggCTATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGCGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAAGAAGA
| | ||| | | | | | | | | | |||| | | | || | |||| | || || | | | | || |||| | | ||| || || | |||| |||| |||| | ||| || ||||||||||| ||||| || || || |||| ||||| || |||||||||||||||||||||||||| | | |||| ||
gtgagcatgctacttgatttatggtct-tatggcatcacataaaaggtgtgcttttaattttttatttggcattcaaccacattatcttataataccgagccactgacttaacttgtatttatatttccatttgtttttcagGCCACGTACAACGAGTTCTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGA-
upper sequence: GLYMA18G44630.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G010453_T01 (Zea mays), 3'ss of exon 1
-------tacaactataataacactttgttttgtttttcatagtatg-gagcgaatgatttcaagtatgttat--gattat-taggttaattataca----ctttatctttgctgacatccttctttctgcttgt-----aggCTATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGCGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAAGAAGA
| | ||| | | | | | | | | | |||| | | | || | |||| | || || | | | | || |||| | | ||| || || | |||| |||| |||||| ||| || ||||||||||| ||||| || || || |||| ||||| || |||||||||||||||||||||||||| | | |||| ||
gtgagcatgctacttgatttatggtct-tatggcatcacataaaaggtgtgcttttaattttttatttggcattcaaccacattatcttataataccgagccactgacttaacttgtatttatatttccatttgtttttcagGCTACGTACAACGAGTTCTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGA-
upper sequence: GLYMA18G44630.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G068151_T01 (Zea mays), 3'ss of exon 3
tacaactataataacactttgttttgtttttcatagtatggagcgaatgatttcaagtatgttatgattattaggttaattatacactttatctttgctgacatccttctttctgcttgtaggCTATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGCGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAAGAAGA
|| || |||| ||| | | || | | || | | || || | | | || | | | | || | ||| | || ||| | || |||| ||||| | ||||||||||| ||||| || || || |||| ||||| || |||||||||||||||||||||||||| | | |||| ||
----gtgatcatgctacttgatttatggtcttatgggctatggcatcacacaaaaggtgtgcttttaataccgagccgctgacttaacttgtattt----atatttccatttgttttt-cagGCCATGTACAGCGAGTTCTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGA-
upper sequence: GLYMA18G44630.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G079117_T01 (Zea mays), 3'ss of exon 1
---------------------tacaactataataacacttt---gttttgtttttcatagtatggagcgaatgatttcaagtatgttatgattattaggtt-aattatacactttatctttgctgacatccttctttctgcttgtaggCTATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGCGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAAGAAGA
| ||| | ||| | | || |||| || | | | ||||| | |||| |||| | | |||| | | | | | || | | || | || |||| || || || ||||||||||| ||||| || || || |||| ||||| || |||||||||||||||||||||||||| | | |||| ||
gtgagcatgctacttgatttatggtcttatggcatcacacaaaaggtgtgcttttaattttttttatttggca--ttcaaccacattatc-ttataataccgagccgctgacttaacttgtatttatatt-tccatttggttttcagGCCATATACAACGAGTTCTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGA-
upper sequence: GLYMA18G44630.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G380227_T02 (Zea mays), 3'ss of exon 2
------------------------------tacaact-ataataacactttgttttgtttttcatagtatggagcgaa-----tgatttcaagtatgttatgattattaggtta----attatacact---------ttatctttgctgacatccttctttctgcttgt-----aggCTATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGCGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAAGAAGA
| || | | || |||| ||| | | || | || | || || ||| || | | | | ||| | || || | | | ||| ||| || | |||| |||| |||| ||||| || ||||||||||| ||||| || || || |||| ||||| || |||||||||||||||||||||||||| | | |||| ||
gtctagctttcttgcatgatgaaggaccctttcaggtgagcatgctacttgatttatggtcttatggcatcacacaaaaggtgtgcttttaattttttatttggcattcaaccacaatatcttataataccgagctgctgacttaactggtatttatatttccatttgtttttcagGCCATGTACAACGAGTTCTCAACT-TGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGAT
upper sequence: GLYMA18G44630.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G143790_T01 (Zea mays), 3'ss of exon 1
-------tacaactataataacactttgttttgtttttcatagtatg-gagcgaatgatttcaagtatgttat--gattat-taggttaattataca----ctttatctttgctgacatccttctttctgcttgt-----aggCTATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGCGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAAGAAGA
| | ||| | | | | | | | | | || | | | | || | |||| | || || | | | | || |||| | | ||| || || | |||| |||| |||| ||||| || ||||||||||| ||||| || || || |||| ||||| || |||||||||||||||||||||||||| | | |||| ||
gtgagcatgctacttgatttatggtct-tatggcatcacacaaaaggtgtgcttttaattttttatttggcattcaaccacattatcttataataccgagccgctgacttaacttgtatttatatttccatttgtttttcagGCCATGTACAACGAGTTCTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGA-
upper sequence: GLYMA18G44630.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G380227_T01 (Zea mays), 3'ss of exon 2
-------tacaactataataacactttgttttgtttttcatagtatg-gagcgaatgatttcaagtatgttat--gattattaggt-taattatac---act-ttatctttgctgacatccttctttctgcttgt-----aggCTATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGCGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAAGAAGA
| | ||| | | | | | | | | | || | | | | || | |||| | || || | | | | | || |||| || | ||| ||| || | |||| |||| |||| ||||| || ||||||||||| ||||| || || || |||| ||||| || |||||||||||||||||||||||||| | | |||| ||
gtgagcatgctacttgatttatggtct-tatggcatcacacaaaaggtgtgcttttaattttttatttggcattcaaccacaatatcttataataccgagctgctgacttaactggtatttatatttccatttgtttttcagGCCATGTACAACGAGTTCTCAACT-TGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGAT
upper sequence: GLYMA18G44630.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G08760.1 (Arabidopsis thaliana), 3'ss of exon 3
tacaactataataacactttgttttgtttttcatagtatggagcgaatgatttcaagtatgttatgattattaggttaattatacactttatctttgctgacatccttctttctgctt-----gtaggCTATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGCGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAAGAAGA
||| | | | | || | || || ||| || | | | | ||| | | ||| | || ||| || |||| ||||| ||||| || || || || || || || | || |||||||||||||| ||||| |||||||| ||||||| || ||| || || ||
-----------------------------------gtacgctaaacaaaactccatcaacatt-tgtgaatttgggtggtaacaaggtttgttgtgattgagcccttttcttcctctgtatgaacagGCAATGTACAATGAATTTTCGACGGCAAATATCCAAGTCGATAAAGATTTCAGCGCCAAGCTATCAGGATACGGTTGTGCAGGCCATGCGCCTGAGACAG-
upper sequence: GLYMA18G44630.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0058g01290.t01 (Vitis vinifera), 3'ss of exon 3
tacaactataataacactttgttttgtttttcatagtatggagcgaatgatttcaagtatgttatgattattaggttaattatacactttatctt-tgctgacatccttctt-tctgcttgtaggCTATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGCGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAAGAAGA
| | ||| | | | | ||| | | | || | | | || || | || | || | | | |||| | | | | | | || || |||||||||| ||||| || ||||| ||||| |||||||||||||| ||||| || ||||||||||| ||||||||||| ||||| || ||||| |||| ||
------------------------tttccctcagatcactgtcccaattctgtatattaggattttttttttccagtggttgttgttcttgttgtgtactgagaacttccctgtgtgtttacagGCTATGTACAATGAATTTTCAACTGCCAATATACAGATTGACAAGGATTTTAGTGCAAAGCTTTCGGGATATGGTTGCGTTGGCCACATTCCAGAAGCAG-Mapped 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|9986583|gb|BE660691.1|BE660691EST: ATGTGCTGCACAAGGTCTAACCTTCTTGCACGAAGAGGGGCCTTTTCAGG CTATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCA
genomic: ATGTGCTGCACAAGGTCTAACCTTCTTGCACGAAGAGGGGCCTTTTCAGGtacaactata ... tgcttgtaggCTATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattaggttaattatacactttatctttgctgacatccttctttctgcttgtaggCTATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGCGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAAGAAGA
tgctgac putative branch site (score: 2)
catccttctttctgct CT-rich tract
ttaattatacacttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacaactataataacactttgttttgtttttcatagtatggagcgaatgatttcaagtatgttatgattattaggttaattatacactttatctttgctgacatccttctttctgcttgtaggCTATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGCGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAAGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG