Sequence
atgc intronic sequence ATGC exonic sequencegttgggagatttctttttcttctaccaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaataacttgacaataagttcatttaagagacaatatttatcttcttgttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTTGGTG
Basic information
species | Glycine max |
transcript | GLYMA12G06530.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G06530.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g62500.1 (Oryza sativa), 3'ss of exon 5
gttgggagatttctttttcttctaccaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaataacttgacaataagttcatttaagagacaatatttatcttcttgttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTTGGTG
|| |||| | | | | | || || || || | || ||| | | |||| | |||| | | || |||| | | || | || || | || | | ||| | | | ||| || ||||||| | | | | ||| | | ||||| ||||| |||||||||||||| || || |||||||||||||| ||||| || ||||| || || || ||||||||||||||||| || |
---------gttagtttttatttgctatttccatctcttgctattttgaacaaaacatgaaattcatatccttt-tttgtaaatgtttgttctgtagctttattcaccattgaca---aagaacatacaataacatattcata-taattctactgaagtaac------------cttgtttc---ttgtgtgctacagGTGTTCTTTAAGGATGTAGCTGGCTGTGATGAAGCCAAACAAGAAATTATGGAATTTGTTCATTTCCTGAAAAATCCCAAGAAATATGAAGAACTGGGAG
upper sequence: GLYMA12G06530.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 5
gttgggagatttctttttcttctaccaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgc--tggtaaataacttgacaataagttcatttaagagacaatatttatcttcttgttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTTGGTG
| | ||| || |||||| | | || || ||| | | | | ||| || || | || || | | | || | | | || | ||| | | | | | || | ||| | ||| | | || | ||| | | |||| || || ||| | | |||||| ||||| ||||| |||||||| || ||||||||||| ||||||||||| || ||||| ||||| || ||||| |||||||| | || |
-----gttagttcattctcttcttctgtt-------ctact-----ttgaaacgactgtca-aatatgaaatatatacatgcacattgattctcaagctctgctagttccacctattcaataatgcagtagctactgcttaaacgtt--gttaagttacaataaaaactgtataatgacaagct-tttctgttggtccagGTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG
upper sequence: GLYMA12G06530.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G038401_T01 (Zea mays), 3'ss of exon 5
gttgggagatttctttttcttctaccaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaat--aacttgacaataagttcatttaagagacaatatttatcttcttgttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTTGGTG
||||| | | || || | ||| || || | | | || || || | || || || || | |||| | || || || | || ||| | | |||||| ||||| || || ||||| || ||||| |||||||| ||||||||||| || ||||| || ||||| ||||| |||||||| | || |
----------------------------------------------------------------------------------ttgttgtagcttcattt---gcccttttcttaagaaacaaagcatactacatgaaattcgaagatttgtcttttcat----caatgtctacttttctgctg-----------gtccagGTGTTTTTTAAGGATGTAGCCGGTTGTGACGAAGCAAAACAAGAAATAATGGAGTTTGTGCATTTCCTTAAAAACCCTAAGAAGTATGAAGATTTGGGAG
upper sequence: GLYMA12G06530.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 5
gttgggagatttctttttcttctaccaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaataacttgacaataagttcatttaagagacaatatttatcttcttgttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTTGGTG
| || | | | | || ||| | | | ||| || ||| | | ||| | |||||| | || ||||| ||||| || ||||||||||| ||||| ||||| || |||||||||||||||||||| || ||||| |||||||||||||| |||||||| | ||||
-------------------------------------------------------------------------------------------------------------gttagagacttagagttttgcctttgtttt--taatga-tccgttt---ggaatttataaacttacttttgttgttt--tcttcgccagATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG
upper sequence: GLYMA12G06530.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G07510.1 (Arabidopsis thaliana), 3'ss of exon 5
gttgggagatttctttttcttctaccaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctgg-taaataacttgacaataagttcatttaagagacaatatttatcttcttgttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTTGGTG
| || || || || | | || | | | ||| | | ||||| | ||||| || || | | ||| |||| ||||| ||||||||||||||||| || || || ||||| || |||||||||||||| ||||| || ||||| |||||||||||||||||||||| | || |
--------------------------------------------------------------------------------------------------gtcagcatttcaatcagggtggagaagttgaattaccatcttcatttccaattcatgatgctattgagattta-ctactgatctattttgttttttgccagATATATTTTAAAGATGTTGCGGGATGCGAGGAGGCTAAACAAGAAATTATGGAATTTGTGCATTTCCTTCAGAACCCAAAGAAATATGAAGATTTGGGAG
upper sequence: GLYMA12G06530.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 5
gttgggagatttctttttcttctaccaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaataacttgacaataagt-tcatttaagagacaatatttatcttcttgttttgtttc--attttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTTGGTG
| || | || |||||| | ||| || ||| | || || || | | | || || | | | | || |||| | | || | | ||| | | | | | | || | | | | ||| | || || | | || | | ||| | | || ||| ||| ||| |||||||||||||| |||||||| |||||||||||||| ||||| ||||| |||||||||||||| || || ||||||||||| | || |
---gttagctaactgtttcttttgtcaa--aggtggtt--tgtctttagtttgcagcatc-caatatttttacagtatacaataattattatatcctccttgctca---cctatggttataatcattcgattttctctctctgactattattattattatcattattattgtttgtttatctatttttggacctagtacagGTCTTTTTCAAAGATGTTGCTGGATGTGATGAAGCAAAGCAAGAAATCATGGAATTTGTTCACTTCCTCAAGAATCCTAAAAAATATGAAGAGTTGGGAG
upper sequence: GLYMA12G06530.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S346_22V6.1 (Physcomitrella patens), 3'ss of exon 6
gttgggagatttctttttcttctaccaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagt-tatttcctccaggcaggagtgct-ggtaaataacttgacaataagttcatttaagagacaatatttatcttcttgttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTTGGTG
| || ||| | | | | | | || | | |||| | | ||| || || ||| | | | | |||| ||| || | ||| | || |||||||||||||| ||||| |||||||| ||||| ||||||||||| || ||||| | || ||||| ||||| ||| | ||||||||||
---------------------------------------------------------------------------------------aagttataagtgggaacatgtcgcgtatggccatgtacatttggtacagtagttgc--atttgtctttttgaaaagaggtgt----------attttatttgatcct-cacagGTAATGTTCAAAGATGTTGCTGGTTGTGACGAGGCAAAACAAGAGATTATGGAGTTCGTTCACTTTTTGAAAAACCCCAAGAAGTATCAGGAACTTGGTG
upper sequence: GLYMA12G06530.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S456_6V6.1 (Physcomitrella patens), 3'ss of exon 6
gttgggagatttctttttcttctaccaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttat-ttcctccaggcaggagtgctggtaaataacttgacaataagttcatttaagagacaatatttatcttcttgt-tttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTTGGTG
| | || || | |||| | || | ||| | || | | | | | | | | | | || | || ||| | |||| | | | ||| | || ||||||||||| || ||||| |||||||| ||||| ||||||||||| || ||||| | |||||||| ||||| || ||||||||||||
------------------------------------------------------------------------------------------------ggatgagagatgctgttccatgatggtgagctatttgccaa--taatga-agacgtactaggggtagagttttgtttttgatgtatctgttgtgtcat-tacagGTTATGTTCAAAGATGTTGCCGGTTGTGACGAGGCAAAACAAGAGATTATGGAGTTCGTTCACTTTTTGAAGAACCCCAAGAAGTACCAAGAACTTGGTG
upper sequence: GLYMA12G06530.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S39_149V6.1 (Physcomitrella patens), 3'ss of exon 5
gttgggagatttctttttcttctaccaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaataacttgacaataagttcatttaagagacaatatttatcttcttgttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTTGGTG
|| | | ||| || | | | || ||| || || || |||| | | ||| | || |||||||||||||| || || |||||||| ||||| || ||||| ||||| |||||| | ||||| || ||||||||| |||||||||| |
--------------------------------------------------------------------------------------------------------------------------------gtga-tgtctt----atgactcccggaaaatgacggagctttattttgtgcgttgtgttgctg----cagGTGATGTTCAAAGATGTTGCTGGTTGCGACGAGGCAAAACAAGAGATCATGGAATTTGTTCACTTCTTGAAGAATCCCAAGAAATATCAAGAACTTGGGG
upper sequence: GLYMA12G06530.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ31204 (Selaginella moellendorffii), 3'ss of exon 6
gttgggagatttctttttcttctaccaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaataacttgacaataagttcatttaagagacaatatttatcttcttgttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTTGGTG
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--------------------------------------------------------------------------------------------------------------------------------gtatgtagct--acagcttctttgtttc--------tagcggttgatcaattgtgcctgaaatt-tgcagGTCACTTTCAATGATGTCGCTGGTTGTGACGAAGCCAAGGAAGAGGTTATGGAATTTGTCCACTTCCTGAAGAATCCCAAGAAGTACGAAGAACTTGGCG
upper sequence: GLYMA12G06530.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ17143 (Selaginella moellendorffii), 3'ss of exon 5
gttgggagatttctttttcttctaccaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaataacttgacaataagttcatttaagagacaatatttatcttcttgttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTTGGTG
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--------------------------------------------------------------------------------------------------------------------------------gtatgtagct--acagttactttttttc--------tagcggtttatcaattgtgcctgaaatt-tgcagGTCACTTTCAATGATGTCGCTGGTTGTGACGAAGCCAAGGAAGAGGTTATGGAATTTGTCCACTTCCTGAAGAATCCCAAGAAGTACGAAGAACTTGGCGMapped 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|163923237|gb|EH039651.1|EH039651EST: ACATAGGAAAAGCACCAGTTACTAAAGTAGACAAAAATGCCAAAAACAAG ATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATG
genomic: ACATAGGAAAAGCACCAGTTACTAAAGTAGACAAAAATGCCAAAAACAAGgttgggagat ... ttttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATG
EST:
gi|16282080|gb|BI944826.1|BI944826EST: ACATAGGAAAAGCACCAGTTACTAAAGTAGACAAAAATGCCAAAAACAAG ATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATG
genomic: ACATAGGAAAAGCACCAGTTACTAAAGTAGACAAAAATGCCAAAAACAAGgttgggagat ... ttttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATG
EST:
gi|22522573|gb|BU081384.1|BU081384EST: ACATAGGAAAAGCACCAGTTACTAAAGTAGACAAAAATGCCAAAAACAAG ATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATG
genomic: ACATAGGAAAAGCACCAGTTACTAAAGTAGACAAAAATGCCAAAAACAAGgttgggagat ... ttttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataagttcatttaagagacaatatttatcttcttgttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTTGGTG
tcttcttgttttgttt CT-rich tract
aatatttatcttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgggagatttctttttcttctaccaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaataacttgacaataagttcatttaagagacaatatttatcttcttgttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTTGGTG
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