Sequence
atgc intronic sequence ATGC exonic sequencegtccgttagttaacattgttgtctcctcttgtgctttacagttgtgttaaaattgtaaggtgtgtgtgtttgattcagagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA
Basic information
species | Glycine max |
transcript | GLYMA11G02410.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g35090.1 (Oryza sativa), 3'ss of exon 2
----------gtccgttagt-taacattgttgtctcct----cttgtgcttta--cagttgt--gttaaaattgtaa---ggtgtgtgtgtttgattcagagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA
|| || ||| | | || | | || || | |||| || || ||| ||||| || ||| | |||||||||| | ||| |||||||||| ||| ||||| |||||||| |||| ||||||||||| ||||||||||| ||||| |||||||||||||| ||
cgctgttggtgtatgtcagtacagcgttcgcatgccaagaggctcaaactgaaagtgattgtaggtgctggttttaacttggtgtatgctgttgttgcagAGGGAGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCGAACCTGCAGGTGATCAAGCTCATGCAGAGCTTCAAGTC--------------------
upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g34460.1 (Oryza sativa), 3'ss of exon 2
-------gtccgttagttaacattgttgtctcctcttgtgctttacag-----ttgtgttaaaattgtaag-----gtgtgtgtgtt-tgattca-----gagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA
| || | || ||| | | || || || || | |||| | | || | |||||| || || | || ||||| |||| | || |||||||||| |||| ||||||| |||||| ||||||||||||| || || ||||| || ||||| |||||||||||||| ||
ataataagaccatatgtcttcatc-ctatttcgactgatgaactagaaggatattgtttctcatttcttcatttgtttgtgtgcattgtggtgcatcatagAGGGGGTTTTGTACGCCAAGAAGGACTACAATTTGGCAAAACACCCACAGATTGATGTGCCAAACCTTCAGGTCATCAAGCTCATGCAGAGCTTCAAGTC--------------------
upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g73160.1 (Oryza sativa), 3'ss of exon 2
---------------------gtccgttagttaacattgttgtctcctcttgtgctttacagttgtg--ttaaaattgtaaggtgtgtgtgtttgattcagagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA
| || | | | || | | | || ||| || || || | ||| | | | || |||||||||| | | ||| |||||||||| ||| ||||| ||||||||| || |||||||||| || || ||||||| ||||| |||||||||||||| ||
acatgttttatttgattggtcatgtatttgctgaaggc-ctgaatgatggtacctttatttgttatgagttgaagtgctaatttaattcaactatatgcagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGGTTGATGTGCCCAACTTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC--------------------
upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G050925_T01 (Zea mays), 3'ss of exon 2
-----------------gtccgttagttaacattgttgtctcctct--tgtgctttacagttgtgttaaaattgtaaggtgtgtgtgtttgat---tcagagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA
||| | || | | | |||| | | |||| || | | ||| || | |||||||| | ||||||| || | ||| |||||||||| ||| ||||| ||||||||| ||||||||||||| || || |||||||| ||||| |||||||||||||| ||
gttctatgtatatccatcaccgagaattgaaagcatggtctgatgtgatgtgtgctatgttcatacggtttctgttagtttgatgtgtttgctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCACAGATTGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTCAAGTC--------------------
upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G065237_T01 (Zea mays), 3'ss of exon 2
-------------gtccgttagttaaca------ttgttgtctcctcttgtgctttacagttgtgttaaaattgtaaggtgtgtgtgtttgat---tcagagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA
| || ||| | ||||| | || | ||| ||| | | | ||| || | ||| |||| | ||||||| || | ||| |||||||||| ||| ||||| |||||||| |||| |||||||| || || |||||||| ||||| ||||||||||| || ||
tccaaatttatttgccccttaaactatggattccttgttatacattcatctgcgttatgttcatacgatttctgttagtttgatgtatttgctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC--------------------
upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G043737_T01 (Zea mays), 3'ss of exon 2
-------------gtccgttagttaaca------ttgttgtctcctcttgtgctttacagttgtgttaaaattgtaaggtgtgtgtgtttgat---tcagagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA
| || || | ||||| | || | ||| ||| | || | ||| || | ||| |||| | ||||||| || | ||| |||||||||| ||| ||||| |||||||| |||| |||||||| || || |||||||| ||||| ||||||||||| || ||
tccaaatttatttgccccctaaactatggattccttgttatacattcatctgcgttatgttcatgcgatttctgttagtttgatgtatttgctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC--------------------
upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G171484_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------------------gtccgttagttaacatt---gttgtctcctcttgtgctttacagttgtgttaaaattgtaag-gtgtgtgtgtttgattcagagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA
| |||| || ||| | || | | |||| ||| | | || || | | || | ||||||| ||| | ||| |||||||||| ||| ||||| |||||||| || |||| ||||| || ||| ||||||| ||||| |||||||||||||| ||
gtgagctccttctcctccctcttcgcccgtccccctaggcgcgcccaatataagattatttcattagatttagataccaattcagacattacaagcattagc-aatattcggatcgtgtacgacccaagcccgtccttgtcttagattgagaaccgttcaactttatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC--------------------
upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G446960_T01 (Zea mays), 3'ss of exon 2
---------gtccgttagt--taacattgttgtctcctcttgtgctttacagttgtgttaaaattgtaaggtgtgtg----tgtttgatt-------cagagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA
| |||| || | || | | | | |||| |||| ||| | | ||| ||||| | | ||||||| || | | || |||||||||| ||| ||||| |||||||| || |||||||||| || || ||||||| ||||| |||||||||||||| ||
agacattatacgcattagcaatattcgtattatgtacgaccctagtttatccttgttttaggttgaaggtatatgtaaaactgtttaacttatggtgcagAGGGGGTCTTGTACGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGATGTGCCCAACTTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC--------------------
upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 2
lower sequence: AT5G52650.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------------------------------------------------------------------------------------gtccgttagttaacattgttgtc-tcctcttgtgctttacagttg-----tgttaaaattgtaaggtgtg-tgtgtttgattcagagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA
|| |||||| | | | | | || |||| || || ||| ||| | | ||| | || || | |||| ||||||||||||||||||||||| |||||||| || ||||| || ||| ||||| || || || || ||||| ||||| |||||||| ||||||||
gttcgttcttcttaaatttgttcttagatctctgttttcttcagcttctgtgagtaaattgattcatttttaggcttatgccgatgaacattgtgatttttgaactagtttaggttaactagttatggtagcaattatgatgtttggcttagaaggtgaacattgtgttgattatcatatgttctatgatttttgcagAAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGATCGATGTCCCCAACCTACAAGTGATTAAGCTTATGCAGAGTTTCAAATC--------------------
upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g00310.t01 (Vitis vinifera), 3'ss of exon 2
------------------------gtccgttagttaacattgtt--gtctcctcttgtgctt-tacagttgtgttaaaattgtaaggtgtgtgt-gtttgattcagagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA
|| | || | || || | || ||| || | || | || | || || | | | | ||||| ||||||||||||||||| |||||| ||||||| |||||| || || || || || || ||||| |||||||||||||| || ||| |||||||||||||||| ||
gtatcttacttattctctcactttaaccacgatttgctgtgattcagtgtgttcatgtttttattttattttattgattttatatattttttcttgtttgcttcagAGGGAGTTTGCTATGCGAAAAAGGACTACAATCTCGCGAAACATCCCGATATCGATGTCCCGAATCTGCAGGTTATCAAGTTGATGCAGAGCTTCAAGTC--------------------
upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 2
lower sequence: EFJ29946 (Selaginella moellendorffii), 3'ss of exon 1
gtccgttagttaacattgttgtctcctcttgtgctt-tacagttgtgttaaaattgtaaggtgtgtg------tgtttgattcagagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA
|| || | | | | |||||| | ||| | | || | | || | | | |||| | ||||||| || || || |||||||||| |||||| | |||||||| ||||| ||||| || ||||| |||||||| ||||| |||||||||||||| ||
----gtgaggggatctagct-tctcctggcgcgctcgcgctcacgcatttctaatccgagatttctccccaattgttcggcgcagAGGGCGTCCTCTACGCCAAGAAGGACTACAATCTCCCCAAGCACCCGGAGATCGATGTCCCCAATCTCCAGGTGATCAAGCTCATGCAGAGCTTCAAGTC--------------------
upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 2
lower sequence: EFJ25099 (Selaginella moellendorffii), 3'ss of exon 1
gtccgttagttaacattgttgtctcctcttgtgctttacagttgtgttaaaattgtaaggtgtgtgtgtttgattcagagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA
|| || | | | | | | | | |||| | | | | || | |||| | ||||||| || || || |||||||||| |||||| | |||||||| ||||| ||||| || ||||| |||||||| ||||| |||||||||||||| ||
----gtgaggggatctagctcgcgcatttctcccttttttctaatccgagatttctc---cccaattgttcggcgcagAGGGCGTCCTCTACGCCAAGAAGGACTACAATCTCCCCAAGCACCCGGAGATCGATGTCCCCAATCTCCAGGTGATCAAGCTCATGCAGAGCTTCAAGTC--------------------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|58014465|gb|CX701207.1|CX701207EST: ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG AAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAG
genomic: ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAGgtccgttagt ... ctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgttaaaattgtaaggtgtgtgtgtttgattcagagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA
gtttgat putative branch site (score: 5)
tttgcttt putative PPT
aaaattgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtccgttagttaacattgttgtctcctcttgtgctttacagttgtgttaaaattgtaaggtgtgtgtgtttgattcagagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT