Sequence
atgc intronic sequence ATGC exonic sequencegttgggagatttctttttcttctatcaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaataacttgacaataagttcatttaagagacaatatttatcttctttttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAGCCCAAAGAAATATGAAGAACTTGGTG
Basic information
species | Glycine max |
transcript | GLYMA12G06580.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G06580.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g62500.1 (Oryza sativa), 3'ss of exon 5
gttgggagatttctttttcttctatcaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaataacttgacaataagttcatttaagagacaatatttatcttctttttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAGCCCAAAGAAATATGAAGAACTTGGTG
|| |||| | | | | || || || || | || ||| | | |||| | |||| | | || |||| | | || ||| ||| | ||||||| | ||| | | || | | | || || | | | | | ||| | | ||||| ||||| |||||||||||||| || || |||||||||||||| ||||| || ||||| || | || ||||||||||||||||| || |
---------gttagtttttatttgctatttccatctcttgctattttgaacaaaacatgaaattcatatccttt-tttgtaaatgtttgttctgtagctttattcacc----------------attgacaaagaacat-acaataacat-attcatataattctactgaagtaaccttgtt-tcttgtgtgctacagGTGTTCTTTAAGGATGTAGCTGGCTGTGATGAAGCCAAACAAGAAATTATGGAATTTGTTCATTTCCTGAAAAATCCCAAGAAATATGAAGAACTGGGAG
upper sequence: GLYMA12G06580.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 5
gttgggagatttctttttcttctatcaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgc--tggtaaataacttgacaataagttcatttaagagacaatatttatcttctttttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAGCCCAAAGAAATATGAAGAACTTGGTG
| | ||| || |||||| ||| | |||| | | | | ||| || || | || || | | | || | | | || | ||| | | | | | || | ||| | ||| | | || | ||| | | |||| || || ||| | | |||||| ||||| ||||| |||||||| || ||||||||||| ||||||||||| || ||||| |||| || ||||| |||||||| | || |
-----gttagttcattctcttctt------------ctgttctactttgaaacgactgtca-aatatgaaatatatacatgcacattgattctcaagctctgctagttccacctattcaataatgcagtagctactgcttaaacgtt--gttaagttacaataaaaactgtataatgacaagct-tttctgttggtccagGTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG
upper sequence: GLYMA12G06580.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038401_T01 (Zea mays), 3'ss of exon 5
gttgggagatttctttttcttctatcaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaat--aacttgacaataagttcatttaagagacaatatttatcttctttttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAGCCCAAAGAAATATGAAGAACTTGGTG
||||| | | || || | ||| || || | | | || || || | || || || || | |||| | || |||| || | || ||| | | |||||| ||||| || || ||||| || ||||| |||||||| ||||||||||| || ||||| || | ||| ||||| |||||||| | || |
----------------------------------------------------------------------------------ttgttgtagcttcattt---gcccttttcttaagaaacaaagcatactacatgaaattcgaagatttgtcttttcat----caatgtctac-----ttttctgctg------gtccagGTGTTTTTTAAGGATGTAGCCGGTTGTGACGAAGCAAAACAAGAAATAATGGAGTTTGTGCATTTCCTTAAAAACCCTAAGAAGTATGAAGATTTGGGAG
upper sequence: GLYMA12G06580.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 5
gttgggagatttctttttcttctatcaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaataacttgacaataagttcatttaagagacaatatttatcttctttttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAGCCCAAAGAAATATGAAGAACTTGGTG
| || | | | | || ||| | | | ||| || ||| | | ||||| |||||| | || ||||| ||||| || ||||||||||| ||||| ||||| || |||||||||||||||||||| || ||||| |||| ||||||||| |||||||| | ||||
-------------------------------------------------------------------------------------------------------------gttagagacttagagttttgcctttgtttt--taatga-tccgttt---ggaatttataaacttacttttgttgttt--tcttcgccagATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG
upper sequence: GLYMA12G06580.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G07510.1 (Arabidopsis thaliana), 3'ss of exon 5
gttgggagatttctttttcttctatcaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctgg-taaataacttgacaataagttcatttaagagacaatatttatcttctttttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAGCCCAAAGAAATATGAAGAACTTGGTG
| || || || || | | || | | | ||| | | ||||| | ||||| || || | | ||| |||| ||||| ||||||||||||||||| || || || ||||| || |||||||||||||| ||||| || ||||| ||| |||||||||||||||||| | || |
--------------------------------------------------------------------------------------------------gtcagcatttcaatcagggtggagaagttgaattaccatcttcatttccaattcatgatgctattgagattta-ctactgatctattttgttttttgccagATATATTTTAAAGATGTTGCGGGATGCGAGGAGGCTAAACAAGAAATTATGGAATTTGTGCATTTCCTTCAGAACCCAAAGAAATATGAAGATTTGGGAG
upper sequence: GLYMA12G06580.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 5
gttgggagatttctttttcttctatcaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaataacttgacaataagt-tcatttaagagacaatatttatcttctttttttgtttc--attttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAGCCCAAAGAAATATGAAGAACTTGGTG
| || | || |||||| | |||| || ||| | || || || | | | || || | | | | || |||| | | || | | ||| | | | | | | || | | | | ||| | || || | | || | | ||| | | || ||| ||| ||| |||||||||||||| |||||||| |||||||||||||| ||||| ||||| ||||||||||||| || || ||||||||||| | || |
---gttagctaactgtttcttttgtcaa--aggtggtt--tgtctttagtttgcagcatc-caatatttttacagtatacaataattattatatcctccttgctca---cctatggttataatcattcgattttctctctctgactattattattattatcattattattgtttgtttatctatttttggacctagtacagGTCTTTTTCAAAGATGTTGCTGGATGTGATGAAGCAAAGCAAGAAATCATGGAATTTGTTCACTTCCTCAAGAATCCTAAAAAATATGAAGAGTTGGGAG
upper sequence: GLYMA12G06580.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S346_22V6.1 (Physcomitrella patens), 3'ss of exon 6
gttgggagatttctttttcttctatcaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagt-tatttcctccaggcaggagtgct-ggtaaataacttgacaataagttcatttaagagacaatatttatcttctttttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAGCCCAAAGAAATATGAAGAACTTGGTG
| || ||| | | | | | | || | | |||| | | ||| || || ||| | | | | | ||| ||| || | ||| | || |||||||||||||| ||||| |||||||| ||||| ||||||||||| || ||||| | || | ||| ||||| ||| | ||||||||||
---------------------------------------------------------------------------------------aagttataagtgggaacatgtcgcgtatggccatgtacatttggtacagtagttgc--atttgtctttttgaaaagaggtgtat----------tttatttgatcct-cacagGTAATGTTCAAAGATGTTGCTGGTTGTGACGAGGCAAAACAAGAGATTATGGAGTTCGTTCACTTTTTGAAAAACCCCAAGAAGTATCAGGAACTTGGTG
upper sequence: GLYMA12G06580.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S456_6V6.1 (Physcomitrella patens), 3'ss of exon 6
gttgggagatttctttttcttctatcaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttat-ttcctccaggcaggagtgctggtaaataacttgacaataagttcatttaagagacaatatttatcttctttttttgtttcattttgtt-cagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAGCCCAAAGAAATATGAAGAACTTGGTG
| | || || | |||| | || | ||| | || | | | | | | | | | | ||| | || | | | | | | | || ||| | || ||||||||||| || ||||| |||||||| ||||| ||||||||||| || ||||| | |||| ||| ||||| || ||||||||||||
------------------------------------------------------------------------------------------------ggatgagagatgctgttccatgatggtgagctatttgccaa--taatga-agacgtactaggggtagagt-tttgtttttgatgtatctgttgtgtcattacagGTTATGTTCAAAGATGTTGCCGGTTGTGACGAGGCAAAACAAGAGATTATGGAGTTCGTTCACTTTTTGAAGAACCCCAAGAAGTACCAAGAACTTGGTG
upper sequence: GLYMA12G06580.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S39_149V6.1 (Physcomitrella patens), 3'ss of exon 5
gttgggagatttctttttcttctatcaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaataacttgacaataagttcatttaagagacaatatttatcttctttttttgtttcattttgtt-cagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAGCCCAAAGAAATATGAAGAACTTGGTG
||| | | | | | | | | ||| |||| || | | ||| | ||| | || |||||||||||||| || || |||||||| ||||| || ||||| ||||| |||||| | |||| || ||||||||| |||||||||| |
-----------------------------------------------------------------------------------------------------------------------------------------gtgatgtcttatg-actcccggaaaatgacggagctttattttgtgcgttgtgttgctgcagGTGATGTTCAAAGATGTTGCTGGTTGCGACGAGGCAAAACAAGAGATCATGGAATTTGTTCACTTCTTGAAGAATCCCAAGAAATATCAAGAACTTGGGG
upper sequence: GLYMA12G06580.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ31204 (Selaginella moellendorffii), 3'ss of exon 6
gttgggagatttctttttcttctatcaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaataacttgacaataagttcatttaagagacaatatttatcttctttttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAGCCCAAAGAAATATGAAGAACTTGGTG
||| || || ||| || ||| || ||| | | || | |||| ||| || ||| || ||||| ||||| ||||| || || ||| |||| ||||||| |||||||||||||| |||| || ||||| || ||||||||||| |
--------------------------------------------------------------------------------------------------------------------------------gtatgtagct--acagcttctttgtttctagcg----gttgatcaattgtgcctg---aaatttg--cagGTCACTTTCAATGATGTCGCTGGTTGTGACGAAGCCAAGGAAGAGGTTATGGAATTTGTCCACTTCCTGAAGAATCCCAAGAAGTACGAAGAACTTGGCG
upper sequence: GLYMA12G06580.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ17143 (Selaginella moellendorffii), 3'ss of exon 5
gttgggagatttctttttcttctatcaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaataacttgacaataagttcatttaagagacaatatttatcttctttttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAGCCCAAAGAAATATGAAGAACTTGGTG
||| || || ||| | | || ||| |||||| | | || | |||| ||| || ||| || ||||| ||||| ||||| || || ||| |||| ||||||| |||||||||||||| |||| || ||||| || ||||||||||| |
--------------------------------------------------------------------------------------------------------------------------------gtatgtagct--acagttactttttttctagcg----gtttatcaattgtgcctg---aaatttg--cagGTCACTTTCAATGATGTCGCTGGTTGTGACGAAGCCAAGGAAGAGGTTATGGAATTTGTCCACTTCCTGAAGAATCCCAAGAAGTACGAAGAACTTGGCGMapped 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|16278923|gb|BI943164.1|BI943164EST: AAATGCCAAAAACAAG ATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATG
genomic: AAATGCCAAAAACAAGgttgggagat ... ttttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATG
EST:
gi|26058256|gb|CA801170.1|CA801170EST: ACATAGGAAAAGCACCAGTTACTAAAGTAGACAAAAATGCCAAAAACAAG ATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATG
genomic: ACATAGGAAAAGCTCCAGTTACTAAAGTAGACAGAAATGCCAAAAACAAGgttgggagat ... ttttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataagttcatttaagagacaatatttatcttctttttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAGCCCAAAGAAATATGAAGAACTTGGTG
tttatcttcttttttt CT-rich tract
aatatttatcttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgggagatttctttttcttctatcaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaataacttgacaataagttcatttaagagacaatatttatcttctttttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAGCCCAAAGAAATATGAAGAACTTGGTG
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