Sequence
atgc intronic sequence ATGC exonic sequencegtacattttcatgtgttcttcagaatactgtccccttgttttactttatgatcatactttccaaagttgtgttcggtctgcttatttcttcaatctgagctttcattatgtacttctatagATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG
Basic information
species | Glycine max |
transcript | GLYMA03G01850.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 9
gtacattttcatgtgttcttcagaatactgtccccttgttttactttatgatcatactttccaaa-gttgtgttcggtctgcttatttcttcaatctgagctttcattatgtacttctatagATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG
|||| | | |||| | || | | | || |||||| | | | || | | ||| || || | |||||||||||| ||||| || ||||||||||| |||||||||||||||||||| |||||| || || |||||||| |||||||| ||||||||||||
-------------------------------------gtttctatctcctgtcatccattagagacagtaatttaggtctgtggactgatccatttcttgtttttttttcttatt---atagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG
upper sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 9
gtacattttcatgtgttcttcagaatactgtccccttgttttactttatgatcatactttccaaagttgtgttcggtctgcttatttcttcaatctgagctttcattatgtacttctatagATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG
|||| | | |||| | || | | ||| | ||| | || | | | | | ||||||||| || || || ||||| ||||| ||||||||||||||||| || |||||| ||||| |||||||| ||||| || ||||||||||||
-------------------------------------gtttgcatctgctatcaaatgccatgaaaccactggtgat--actttgtagactaatgtttttctttcccttttgatccaa--gATTTTGGGTACTCCAACAAGAGAGGAAATCAGGTGCATGAATCCAAATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG
upper sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G131853_T01 (Zea mays), 3'ss of exon 9
gtacattttcatgtgttcttcagaatactgtccccttgttttactttatgatcatactttccaaagttgtgttcggtctgcttatttcttcaatctgagctttcattatgtacttctatagATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG
| | || | | | | || |||| || || || | || ||| | | || ||| ||||| | || | |||||||||| || || || ||||| || || ||||||||||||||||| || ||||| ||||| |||||||| ||||| || ||||||||||||
--------------------------gtttgcatctgctatcaaatcgtg-tcatgaaatcactggtggtactttgtaggctgaatgttttt-tcttctctttcttcatcca-------agATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG
upper sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G61160.2 (Arabidopsis thaliana), 3'ss of exon 9
gtacattttcatgtgttcttcagaatactgtccccttgttttactttatgatcatactttccaaagttgtgttcggtctgcttatttcttcaatctgagctttcattatgtacttctatagATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG
|| | ||| ||| ||||| | | | || ||| | || || ||| | | | | ||| | || | || | ||||||| || ||||| | |||||||| |||| | ||||||||| |||||||| |||||||| ||||||||||||||||| || |||||||||
------------------------gtaacaacatattggttt-ttttattac--ttttatctgttgtttttttgggggggctcagattctta----gagtt---gttgtataa----acagATTTTAGGGACACCAGCAAGAGAAGAGATAAAGAACATGAATCCTCGTTACAATGATTTTAAGTTCCCTCAGATCAAAGCTCAGCCGTGGCACAAG
upper sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 9
gtacattttcatgtgttcttcagaatactgtccccttgttttactttatgatcatactttccaaagttgtgttcggtctgcttatttcttcaatctgagctttcattatgtacttctat-agATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG
| || || | || || | | | | ||| | | ||| || | | | |||| ||||| |||| ||||| | || || || || |||||||||||| |||| |||||||| || |||| || || ||||||||||| |||||||||||||| |||||||||
-----------------------------------gtacttaacctgatccctcgtgttccttcatctctcttc--tatatttaatttactagttta----ctcatc-tgtacatctaccagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG
upper sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 9
gtacattttcatgtgttcttcagaatactgtccccttgttttact-ttatgatcatactttccaaagttgtgttcggtctgcttatttcttcaatctgagctttcattatgtacttctatagATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG
| | || || | | ||| || |||| | | |||| | | | | | |||| ||| | || || || ||| | | | |||||| |||| |||||||||||||||||||| | ||||||||||||||| |||||||| || |||||||| || ||||||||||||||||||||||||
----------------------gtttgctatcaagtggcttttctgttattcactttcttttcttaat-attataggtcagctaag-----caggatgttgttgcatgttatgtct---tagATTCTGGGTACACCCACCAGAGAAGAAATTAAGTGCATGAATCCAAATTACAATGAGTTCAAGTTTCCACAAATCAAAGCTCACCCATGGCACAAG
upper sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 8
gtacattttcatgtgttcttcagaatactgtccccttgttttactttatgatcatactttccaaagttgtgttcggtctgcttatttcttcaatctgagctttcattatgtacttctat---agATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG
||| || | | | | | | ||| || | | | || | |||| | | | | | | | | | | | | || | | || | ||||| ||||| || | || || || | |||||||||||| ||||||| || || |||||||| || ||||| |||||||||||||||||
gtagggca-caggcgatgcacggtgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggagtgttatgatgctgtggagtgtatgttattgaggaaaagttttgtggcagGTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA
upper sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 8
---------gtacattttcatgtgttcttcagaatactgtccccttgttttactttatgatcatactttccaaagttgtgttcggtctgcttatttcttcaatctgagctttcattatgtacttctat---agATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG
| | | ||| | ||| || | || ||| || | | | | ||||| | | | | | || | | |||||| | | || | ||||||||||| || | || || |||| |||||||||||| ||||||| || || |||||||| || ||||| |||||||| ||||||||
gtagggcacaggcggtgcacggcgttgtgttgaagggtggcgtac----ttgcttgctggttgtgactgttgcgggggtgttatgatgctgtggagtgtgagtatg--ttattgaggagtacttgtgtggcagGTGTTGGGAACACCGACTCGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCGTGGCACAAA
upper sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------------gtac--at-tttcatgtgttc---ttcagaatactgtccccttgttt----tactttatgatcatactttccaaagttgtgtt-cggtc----tgcttatttcttcaatctgagctt-tcattatgt--------acttctatagATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG
|||| || ||| |||||| || | | || ||| | || | | || || | | || ||||| |||| || | | |||||| | | || | | | | || | || || ||||| || | || || |||| |||||||||||| ||||||| || || ||||||||||| || || |||||||| |||||||||
gtatgttatacatggtagagtggaagcatatggagctgaagtcgtttgtactgatgtttgatgtgtatcgattaaaagtattgtattatatttaaagatgttagctgctcttgttgcttcgggtggtgttgcggtgatagcgcaagagtgatactgtagagcttatgagtaggcggatggtgatgttgacagGTGTTAGGGACACCTACACGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCACCCGTGGCACAAG
upper sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 9
gtacattttcatgtgttcttcagaatactgtccccttgttttactttatgatcatactttccaaagttgtgttcggtctgcttatttcttcaatctgagctt--tcattatgtacttctatagATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG
| ||| | ||| | | | || |||| || ||| | | | | ||| ||| | | ||| | || | || || || || || | || ||||| | ||||||||||||||||||| || |||||||| |||||||| ||||| || || |||||||||
-----------------------------------------------gtacgcatgcattctt--gctcttttttttctgttt-tttttgcgagtcgctcttgctcaagacttgcttttgcagGTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG
upper sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 9
gtacattttcatgtgttcttcagaatactgtccccttgttttactttatgatcatactttccaaagttgtgttcggtctgcttatttcttcaatctgagctt--tcattatgtacttctatagATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG
| ||| | ||| ||| || | || ||| | | | | ||| ||| | | ||| | || | || || || || || | || ||||| | ||||||||||||||||||| || |||||||| |||||||| ||||| || || |||||||||
-----------------------------------------------gtacgcatgcattc-----ttgctctc---ttttttctttttgcgagtcgctcttgctcaagacttgcttttgcagGTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAGMapped 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|51335237|gb|CO979103.1|CO979103EST: CATTGTTTCCTGGAGAGAGTGGGATTGATCAGTTAGTAGAGATCATTAAG ATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTAC
genomic: CATTGTTTCCTGGAGAGAGTGGGATTGATCAGTTAGTAGAGATCATTAAGgtacattttc ... acttctatagATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTAC
EST:
gi|58020603|gb|CX707345.1|CX707345EST: CATTGTTTCCTGGAGAGAGTGGGATTGATCAGTTAGTAGAGATCATTAAG ATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTAC
genomic: CATTGTTTCCTGGAGAGAGTGGGATTGATCAGTTAGTAGAGATCATTAAGgtacattttc ... acttctatagATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtgttcggtctgcttatttcttcaatctgagctttcattatgtacttctatagATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG
tacttct CT-rich tract
ttatttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacattttcatgtgttcttcagaatactgtccccttgttttactttatgatcatactttccaaagttgtgttcggtctgcttatttcttcaatctgagctttcattatgtacttctatagATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA