Sequence
atgc intronic sequence ATGC exonic sequencegtatatagcttttcttgtgcttttcctacatctcagtcctgaacttatatttaacatttgaatactaactattttctttaatctcttgttacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAGTCTA
Basic information
species | Glycine max |
transcript | GLYMA11G18290.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G18290.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g64560.2 (Oryza sativa), 3'ss of exon 6
gtatatagctttt-cttgt-gcttttcctacatctcagtcctgaacttatatttaacatttgaatactaactattttctttaatctcttgttacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAGTCTA
||| | ||| | | | | |||| || | | | || | | | | |||| || || | | | ||| | |||| ||| ||||||||||||| ||| || | ||||| |||||||| ||||||||||||||| |||||| ||| ||||||||||||| ||| |||| | |||||| | |
gta-acagcaccaacacatagatacccctatat-tgacctttaaaataaaacacattattt--atcatatttttggtacttagatttctgtt-tgattaaacagTGTAGCATTGATACATTACTGGAGAAGACCATTAAGCATATGCTTTTCTTGCAAAATGTTGCAAAGCATGCTGATAAGTTGAAGGGATCTGGGGAGCCAA
upper sequence: GLYMA11G18290.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os12g06330.1 (Oryza sativa), 3'ss of exon 6
---------------gtatatagcttttcttgtgcttttcctacatctcagtcctgaacttatatttaac---atttgaatactaactattttct----------ttaatctcttgttacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAGTCTA
| |||| ||| |||| || | || |||| ||| || |||| || || | | || | || ||| ||| | |||||||||||||| |||||| | ||||||||||||| ||||| ||| ||||| |||||||||| || |||||||| ||||| || || | | || || |
gtatcctcttgttcaccctcacactttaaatgtcctttatgattatttagatcttgaatcc-cattgaatttagtttggatgtaaattctgttgtgtgctgatggctagcctcatgtcaattgccaacagTGTAGCATTGATGCATTATTGGAAAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACGAAGCATGCAGACAACCTCAAGGATTCTAACGAATCAA
upper sequence: GLYMA11G18290.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g06010.1 (Oryza sativa), 3'ss of exon 6
--------------------------gtatatagcttttcttgtgcttt---tcctacatctcagtcctgaacttatatttaacatttg-aatactaact-attttctttaatctcttgttacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAGTCTA
|| ||| |||| | || ||| || || || |||||||| || |||| ||| | ||| || | | ||| | | || |||||||||||||||| ||||| | ||||| ||||| | ||||| ||||||||| |||||||||| || |||||||| |||||||| || | | || || |
gtatcctctaatgaatctttctggttttaaataactttcatggtaatttgcactttatatagcatatttgaacttaagagcaatttttgcaatgttgacttgttaattgtgatcgcattttt---ttcaacagTGTAGCATCGATGCCTTGCTGGAGAAGACAGTTAAGCACATGCTTTTCTTGCAAAGTGTGACGAAGCATGCAGACAAGCTCAAGGATTCTACTGAATCCA
upper sequence: GLYMA11G18290.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G069408_T01 (Zea mays), 3'ss of exon 6
------------------------gtatatagcttttcttgtgcttttcctacatctca-gtcc---tgaacttatatttaacatttgaatacta--actattttctttaatctcttgttacaat---tcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAGTCTA
| | | | || | || ||| || | | || | || |||| | | ||| || | ||| || || ||| |||| | | |||||||||||| || |||||| | ||||| |||||||| ||||| ||||||||| |||||||||| ||||||||||| || || || || | || | |||
gtatcctcttcttctactcacgcatttcaaacgtgttttagtaatttagggttatttaatgttcaattgcacttgtttcaaac-ttcatacacttgtacgatgactgttagtctcacagcattttttgtcaacagTGTAGTATTGATGCATTACTGGAGAAGACCATTAAGCACATGCTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAACAAATCTG
upper sequence: GLYMA11G18290.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G031656_T01 (Zea mays), 3'ss of exon 6
--------------------------------gtatatagcttttcttgtgcttttcctacatct-cagtcctgaacttatatttaacat--ttgaatactaactattttctttaatctcttgttacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAGTCTA
|| | | | | | | || || | || | | | || | || ||| | | ||| || | || | | || ||||||||||||||| ||||| | |||| |||||||| ||||| ||| ||||| |||||||||| ||||||||||| || || || || | || || ||||
gtatcctcttcttctacttgtgcatttcaaatgtgtgttaggaatttaggattatttaaggttcaatggcacttgtttgaaacttcatatgcttgtgcaatgactgttaagcctcataacattttttg--tcaacagTGTAGCATTGATGCCTTGTTGGAGAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAATGAATCTA
upper sequence: GLYMA11G18290.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G031656_T02 (Zea mays), 3'ss of exon 7
--------------------------------gtatatagcttttcttgtgcttttcctacatct-cagtcctgaacttatatttaacat--ttgaatactaactattttctttaatctcttgttacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAGTCTA--
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gtatcctcttcttctacttgtgcatttcaaatgtgtgttaggaatttaggattatttaaggttcaatggcacttgtttgaaacttcatatgcttgtgcaatgactgttaagcctcataacattttttg--tcaacagtgtagCATTGATGCCTTGTTGGAGAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAATGAATCTAAG
upper sequence: GLYMA11G18290.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0009g00440.t01 (Vitis vinifera), 3'ss of exon 6
gtatatagcttttcttgtgcttttcctacatctcagtcctgaacttatatt-taacatttgaatactaactattttctttaatctcttgttacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAGTCTA
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----gtaactcatctttcttcctttcttcctcacttttttgaggacattttactatattgagatactgattatgtcctctaatctactgatgtggtttaacagTGTAGCATTGATGCACTGCTTGAACGCACCATCAAGCATATGCTTTTCTTGCAAAGTGTCATGAAGCATGCAGACAAGCTAAAGCAAACTGGAGAGTCTAMapped 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|207698174|gb|GD679559.1|GD679559EST: TTCAAGATCGTGTAAAAGAGTTGCGGGAAATTGTGCCAAATGGAGCAAAA TGTAGCATAGATGCACTTCTGGAA
genomic: TTCAAGATCGTGTAAAAGAGTTGCGGGAAATTGTGCCAAATGGAGCAAAAgtatatagct ... aattcaacagTGTAGCATAGATGCACTTCTGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttaacatttgaatactaactattttctttaatctcttgttacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAGTCTA
atttgaatactaacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatagcttttcttgtgcttttcctacatctcagtcctgaacttatatttaacatttgaatactaactattttctttaatctcttgttacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAGTCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA