Sequence
atgc intronic sequence ATGC exonic sequenceAGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAGCATAATGAAATTCAGACTGTCAATATAAAAAGTGTAGGAGCAGATGTAGAGgtatgggctctgttattcctttttttttttgggctgtataatttgcgagcaagaagtgttaagttctctttatttttagtgacatgtgcaagtactatgcttcttag
Basic information
species | Glycine max |
transcript | GLYMA13G43680.1 |
intron # | 10 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 10
AGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAGCATAATGAAATTCAGACTGTCAATATAAAAAGTGTAGGAGCAGATGTAGAGgtatgggc-tctgttattcctttttttttttgggctgtataatttgcgagcaagaagtgttaagttctctttatttttagtgacatgtgcaagtactatgcttcttag
||||||||| ||||||||||||| ||| || ||||| || ||||| || ||||||||||| || ||||| ||||| || | | | || ||||| ||||| | | || | | | || |||||| ||| | | | |||| | | || | || | |
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttttcttgttcaccatgctaatatgttgaaaacttgtatactttctta-tacgtcttgtttactaacctgttccatttttcag------------------------
upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 1
AGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAGCATAATGAAATTCAGACTGTCAATATAAAAAGTGTAGGAGCAGATGTAGAGgtatgggctctgttattcctttttttttttgggctgtataatttgcgagcaagaagtgtt----aagttctctttatttttagtgacatgtgcaagtactatgcttcttag
||||||||| ||||||||||||| ||| || ||||| || ||||| || ||||||||||| || ||||| ||||| || | | | || ||||| ||||| | | || | | | || |||| | || | | | |||| || | | | |||| ||
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttttctgttcaccatgctaatatgttgaaaacttgtaatactttcttatacgtcatgtttcctaacctgttctatttttcag----------------------------
upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 10
AGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAGCATAATGAAATTCAGACTGTCAATATAAAAAGTGTAGGAGCAGATGTAGAGgtatgggctctgttattcctttttttttttgggctgtataatttgcgagcaagaagtgttaagttctctttatttttagtgacatgtgcaagtactatgcttcttag
||||||||| ||||||||||| | ||| || |||||||| ||| | |||||||||||||| || ||||| ||||| || ||||| || ||||| ||||| | || |||| | | | || | |||| | || | ||| | | ||| | ||| | | | | || | || | ||
AGTTCCTGTTGCTAGCATGGATAGCAGTGGAAAAATTATATGGGCAAAGCATAATGAAATCCAAACTGTTAATATCAAGAGTGTTGGTGCAGACAATGAGgtt--gcctttgtt----caccatgctgctgcgatgtaaacttagtaagcttg---ttataaagtttctctgtggtccttaactgtttcattttttag---------
upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 10
AGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAGCATAATGAAATTCAGACTGTCAATATAAAAAGTGTAGGAGCAGATGTAGAGgtatgggctctgttattcctttttttttttgggctgtataatttgcgagcaagaagtgttaagttctctttatttttagtgacatgtgcaagtactatgcttcttag
||||||||| ||||||||||| | ||| || |||||||| ||| | |||||||||||||| || ||||| || || || ||||| || ||||| ||||| | || |||| | | | || | | |||| | || | ||| | | |||| | ||| | | | | | | || | ||
AGTTCCTGTTGCTAGCATGGATAGCAGTGGAAAAATTATATGGGCAAAGCATAATGAAATCCAAACTGTTAACATCAAGAGTGTTGGTGCAGACAATGAGgtt--gcctttgttcaccatgctattat----gatgtaaacttagtaagcttg---ttataaggtttctctgtggtccttaattgtttcattttttag---------
upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 10
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 10
AGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAGCATAATGAAATTCAGACTGTCAATATAAAAAGTGTAGGAGCAGATGTAGAGgtatgggctctgttattcctttttttttttgggctgtataatttgcgagcaagaagtgttaagttctctttattt--ttagtgacatgtgcaagtactatgcttcttag
| ||||||| |||||||||||||| | ||| ||||| || ||| ||||||||||||||||||| |||| || || |||||| | || |||||| |||||| || | ||| | | || |||| || || | || | || || | || || | ||| | || || || | |||||
AATTCCTGTCGCTAGCATGGACAATACCGGAAAAATCATATGGGCTAAGCATAATGAAATTCAAACTGCAAACATCAAAAGTATTGGTGCAGATTACGAGgtacacgccata------cttgtaactcttatactgtggcat-----aggatgacctatttgttttttgtttttcgcctgatgataagtttttgttctgtaa--cttag
upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 10
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 14
---AGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAGCATAATGAAATTCAGACTGTCAATATAAAAAGTGTAGGAGCAGATGTAGAGgtatgggctctgttattcctttttttttttgggctgtataatttgcgagcaagaagtgttaagttctctttatt-tttagtgacatgtgcaagtactatgcttcttag
| | || |||||||| ||||| |||||||| |||||||||||| |||| || ||||| || || ||||| || || || ||||| || ||||||| |||| |||| | | | | ||| || ||| ||| || || | | |||| | | ||||| ||| || | | ||
TGAAATACCAGTGGCTAGTATGGATAACAGCGGAAAAATTATTTGGGCTAAACACAATGAGATACATACTGTAAACATCAAGAGTGTGGGCGCAGATG---AGgtttggggttta--acacttttacattgttgccttgtgtatttgaaaattagctcatgtttggcaatgtttatcatttggttctgagcctacttag------------
upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 10
lower sequence: AT3G15980.5 (Arabidopsis thaliana), 5'ss of exon 10
AGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAGCATAATGAAATTCAGACTGTCAATATAAAAAGTGTAGGAGCAGATGTAGAGgtatgggctctg-ttattcctttttttttttgggctgt-ataatttgcgagcaagaagtgttaagttctctttatttttagtgacatgtgcaagtactatgcttcttag
| ||||||| ||||||||||||| ||||| ||||| || ||| ||||||||||||||||||| || | || || |||||| | || |||| | ||||| | | || || | || || | || ||| || | || |||| | | | || | || | | | | | | |
AATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAGCATAATGAAATTCAAACCGCAAACATCAAAAGTATTGGTGCAGGTTACGAGgtctagctcctaattgtaactcttgtattctggcatgggaaaacctgcgtgactcagctatttatttgtactgcctgatgattttaag---------------------
upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 10
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 10
AGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAGCATAATGAAATTCAGACTGTCAATATAAAAAGTGTAGGAGCAGATGTAGAGgtatgggctctg-ttattcctttttttttttgggctgt-ataatttgcgagcaagaagtgttaagttctctttatttttagtgacatgtgcaagtactatgcttcttag
| ||||||| ||||||||||||| ||||| ||||| || ||| ||||||||||||||||||| || | || || |||||| | || |||| | ||||| | | || || | || || | || ||| || | || |||| | | | || | || | | | | | | | | || | |||||
AATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAGCATAATGAAATTCAAACCGCAAACATCAAAAGTATTGGTGCAGGTTACGAGgtctagctcctaattgtaactcttgtattctggcatgggaaaacctgcgtgactcagctatttatttgtactgcctgatgattttaagctttcat-ctctctaccttag
upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 10
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 10
AGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAGCATAATGAAATTCAGACTGTCAATATAAAAAGTGTAGGAGCAGATGTAGAGgtatgggctctgttattcctttttttt-tttgggctgtataatttgcgagcaagaagtgttaagttctctttatttttagtgacatgtgcaagtactatgc-ttcttag
||| |||||||| || ||||||||||| || ||||| || ||| ||||||||||||||||||||||||| |||||||| ||||| ||||||||| | ||||| || || | ||| || | ||| || | || | | ||| ||||| || | || || | | | | | | |||| |||| ||
AGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAGCATAATGAAATTCAGACTGTGAATATAAAGAGTGTGGGAGCAGATTTTGAGgtttgaacttaaattcagcttattctcattttggttacatgacattgaagctt-aagtgagaaatccttaaggttcacatttctttct-----tgccatgccttctcagMapped 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|9987279|gb|BE661387.1|BE661387EST: ATAATGAAATTCAGACTGTCAATATAAAAAGTGTAGGAGCAGATGTAGAG GTTGCTG-CNGAGAAAGGTTACCTTTAGCTGGTAAGGAGTTTGGGTACCTG
genomic: ATAATGAAATTCAGACTGTCAATATAAAAAGTGTAGGAGCAGATGTAGAGgtatgggctc ... tgcttcttagGTTGCTGACGGAGAAAGGTTACCTTTAGCTGTTAAGGAGTT-GGGTACCTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAGCATAATGAAATTCAGACTGTCAATATAAAAAGTGTAGGAGCAGATGTAGAGgtatgggctctgttattcctttttttttttgggctgtataatttgcgagcaagaagtgttaagttctctttatttttagtgacatgtgcaagtactatgcttcttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG