Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttttgtggatagaatttttgcaattaatttcttaatataattttttaagcccttgaatagtgctgagtgggaagctgtgccaaattgtgcctgaattatgaaattttcttatccttaactcttttctcgtatcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAG
Basic information
species | Glycine max |
transcript | GLYMA13G43680.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 9
gtaagttttttgtggatagaatttttgcaattaatttcttaatataattttttaagcccttgaatagtgctgagtgggaagctgtgccaaattgtgcctgaattatgaaattttcttatccttaactcttttctcgtatcggg------tgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAG
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------------------------------------------------------------caatttgctcttcacagaaacccttttcttttcatgttttcatta--acttcttccttttcaagttaatttagtgatacgggaaaaaacttgacttgtgcagGGTTGTGATCGGATATGATGAAGGGACAATAATGATAAAAATTGGCCGTGAAGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAA
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 9
gtaagttttttgtggatagaatttttgcaattaatttcttaatataattttttaagcccttgaatagtgctgagtgggaagctgtgccaaattgtgcctgaattatgaaattttcttatccttaactcttttctcgtatcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAG
| ||||| | | ||||| || || ||| || | | |||| | | | || | ||| || | | | | | | || |||||||||||||| ||||||||||| ||||| ||| | ||| ||||||| ||||||||||| ||||||||||| | ||| || |||||||| ||| | |||
------------------------------------------aagaatttctc---tcattgaaacatgttgtgtgagatttt-cattgacttgttctttcctgcataagtcaagttaatgatatggaatattttattttgtgt----------agGGTTGTGATTGGATATGATGAAGGGACAATAATGATAAAAATTGGTCGTGAAGTTCCTGTTGCTAGCATGGATAGCAGTGGAAAAATTATATGGGCAAAG
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 9
gtaagttttttgtggatagaatttttgcaattaatttcttaatataattttttaagcccttgaatagtgctgagtgggaagctgtgccaaattgtgcctgaattatgaaattttcttatccttaactcttttctcgtatcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAG
|| | | | | | | || || | || ||| || | ||||| || || | | | | || | || | | | | | || |||||||||||||| || |||||||| ||||| ||| | ||| ||||||| ||||||||||| ||||||||||| | ||| || |||||||| ||| | |||
------------------------------------------taaagatatgttatcactgaaaca----tgtgtgaga-----tttttaattg-gcttgttcttt----cctgcataagtcaagctaatggcatggaaaaacttattttgtgtagGGTTGTGATTGGATACGATGAAGGGACAATAATGATAAAAATTGGTCGTGAAGTTCCTGTTGCTAGCATGGATAGCAGTGGAAAAATTATATGGGCAAAG
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 9
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagttttttgtggatagaatttttgcaattaatttcttaatataattttttaagcccttgaatagtgctgagtgggaagctgtgccaaattgtgcctgaattatgaaattttcttatccttaactcttttctcgtatcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAG
||| | | | || | | | || | | || || | | || | || || | || ||| || || | | ||||||||||||| || |||||||||||||| || ||||| |||||||| |||||| ||||||| |||||||||||||| | ||| ||||| || ||| |||||
--------------------------------------------------cttagatttgttagaaatgata--ttgagaggtctacctggttctag-tactccattgagttgtcctgca---aaaccttaccttgtccacattctcatttcacagGGTTGTGATCGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAATACCGGAAAAATCATATGGGCTAAG
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 9
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaagttttttgtggatagaatttttgcaattaatttcttaatataattttttaagcccttgaatagtgctgagtgggaagctgtgccaaattgtgcctgaattatgaaattttcttatccttaactcttttctcgtatcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAG
|||||||| | | | | | ||| ||| | || || | | | || | | || | | | | |||| || || || | | || || || | || | || | || ||||||||| ||||| ||||| |||||| | || ||||| |||||||| || ||| | || |||||||| ||||| |||||||| |||||||||||| ||||
gtaagtttctgatcttttactatgtcaatatttattccctattaaagatatata--tcttcacatcataattatttc---tttgtgtaaatttatgtttccttcat--aacttacgagatggcaataccttgtctttttc-------------cagGGTTGTAATTGGTTATGACGAAGGATCCATAATGGTGAAACTTGGCCGTGAAATACCAGTGGCTAGTATGGATAACAGCGGAAAAATTATTTGGGCTAAA
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 9
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaagttttttgtggatagaatttttgcaattaatttcttaatataattttttaagcccttgaatagtgctgagtgggaagctgtgccaaattgtgcctgaattatgaaattttcttatccttaactcttttctcgtatcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAG
| | | || | |||| || | | | | ||| |||| ||| | | || | || | | | | || | | ||||||||||||||| |||||||||||||| || ||||| |||||||| |||||| ||||||| ||||||||||||| ||||| ||||| || ||| |||||
-----------------------------------------------------agggcgtttag-agtggctaggagttttttagggatcagtgttagcaccttattaaactga-tcatacgggaccatcaacaacgaatgtgtttgcttta-cagGGTTGTGATTGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAG
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 9
gtaagttttttgtggatagaatttttgcaattaatttcttaatataattttttaagccct-tgaatagtgctgagtgggaagctgtgccaaattgtgcctgaattatgaaattttcttatccttaactcttttctcgtatcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAG
| || | | | || | | ||| | || || | | | | || || ||| || | | | | ||| || | | | || ||||||||| || |||||||||||||||| |||||||| ||||||||| ||||||| |||||||| || ||||||||||| || ||||| || ||| |||||
----------------------------------tgtcacacttcacttctcttgttcctgtagccagcactaaat-------------atttagtatatggcttaggagaaatggcttggaatgactattattgctc----------tccatccagGGTTGTAATCGGCTATGATGAAGGAAGTATTATGGTAAAACTTGGTAGAGAAGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAG
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 9
gtaagttttttgtggatagaatttttgcaattaatttcttaatataattttttaagcccttgaatagtgctgagtgggaagctgtgccaaattgtgcctgaattatgaaattttcttatccttaactcttttctcgtatcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAG
|||||| ||| | ||||||| | | | | || | ||| | | || | | ||| | | | || ||| || | | | | || ||||||||||||| || | |||||||||||| |||||||| ||| |||||||||| | || || ||||| ||||| || || || || || || ||| ||||
--------------------------------------aaaatataggtttat-----tttgaataattgttatc---acactctctcaa--tatagttg--ctgtatgctttattcacatgtggcttctttttctttcc---tacttt---acagGGTTGTGATCGGTTTTGATGAAGGAACCATTATGGTGAAAATTGGTCGAGATGAACCAGTAGCTAGTATGGATAATAGTGGAAAGATCATATGGGCTAAAMapped 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: TATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCG GGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGA
genomic: TATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCGgtaagttttt ... attcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatgaaattttcttatccttaactcttttctcgtatcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAG
ccttaac putative branch site (score: 3)
aaattttcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttttttgtggatagaatttttgcaattaatttcttaatataattttttaagcccttgaatagtgctgagtgggaagctgtgccaaattgtgcctgaattatgaaattttcttatccttaactcttttctcgtatcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA