Sequence
atgc intronic sequence ATGC exonic sequencegtatctatgaaatgatatttatgttaggtgctgtgagtaggttgttactactattagtagttactaatttctgatgggctgctgtgaattagtttttgtttctcttaacctctagctatttggttgggctacacttccctatgattttagatattttctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
Basic information
species | Glycine max |
transcript | GLYMA11G31470.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 3
gtatctatgaaatgatatttatgttaggtgctgtgagtaggttgttactactattagtagttactaatttctgatgggctgctgtgaattagtttttgtttctcttaacctctagctatttggttgggctacacttccctatgattttagatattttctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
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------------------------------------------------------------------------------------------agggatttacacagatattgtcgagaatattttatgaaattcctatgcttgaaggttgaagtatttctcaccatgt--gtttttttaa--aatgtcgaatgcagATGGATGGATTTGATCAAACAGTGAATGTGAAGGTTATAATGGCGACCAACAGGGCGGATACCCTAGACCCTGCTCTGTTACGTCCAGGTAGATTGGACA
upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 3
gtatctatgaaatgatatttatgttaggtgctgtgagtaggttgttactactattagtagttactaatttctgatgggctgctgtgaattagtttttgtttctcttaacctctagctatttggttgggctacacttccctatgattttagatattttctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
|| | | ||||| | || | | ||| | | || | |||| | | | | ||| | | | | | | ||| || | | ||||||||||| ||||| |||||||| ||||| || ||||| ||||||||||| | ||||||||| | || |||||||||||||||||||| || |||||
------------------------------------------------------------------------------tctctaaaagcaaacttttg--------gagttccaacagtttt-ctagattatagttcctactagctctttttgtttctt--attagtaatgttgttatctatgtta-----cagATGGATGGGTTTGATCAAACAGTGAATGTGAAGGTTATAATGGCAACTAATCGGGCAGACACTCTAGATCCTGCTCTGTTGCGTCCTGGTAGACTTGACA
upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 3
gtatctatgaaatgatatttatgttaggtgctgtgagtaggttgttactactattagtagttactaatttctgatgggctgctgtgaattagtttttgtttctcttaacctctagctatttggttgggctacacttccctatgattttagatattttctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
|| | || ||| | || || || || | | || | |||| | |||| ||||| | | | | | | ||| | | | ||||||||||| ||||| |||||||| ||||| || ||||| ||||||||||| | ||||||||| | || |||||| ||||||||||||| || |||||
------------------------------------------------------------------------------tctctaaaagctaactttgggaattccta---------tagtttcctagattataattcctactagttttttttatttctt--attagtaatgtggttatttatgttg-----cagATGGATGGGTTTGATCAAACAGTCAATGTGAAGGTTATAATGGCAACTAATCGGGCAGACACTCTAGATCCTGCTTTGTTGCGTCCTGGTAGACTTGACA
upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G58290.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatctatgaaatgatatttatgttaggtgctgtgagtaggttgttactactattagtagttactaatttctgatgggctgctgtgaattagtttttgtttctcttaacctctagctatttggttgggctacacttccctatgattttagatattttctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
|| | | ||| | |||| ||| || | ||| ||| | || | | |||||||| | | | || || | ||| | || | |||||||||| |||||||| || || ||||| || || || |||||||| ||||| ||||||||| | || |||||||| || ||||||||||| |||||||
-------------------------------------------------------------------------gtgaga-acaaataatgaattttagttgtaattcagatct---tatgttgtagaataatg---------gattttagttgtgtccttaa--------cttattgtgttgaattcgatgtagATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAACAGGGCAGACACTCTAGATCCTGCTCTCTTACGTCCTGGAAGACTTGATC
upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 3'ss of exon 3
gtatctatgaaatgatatttatgtta-ggtgctgtgagtaggttgttactactattagtagttactaatttctgatgggctgctgtgaattagtttttgtttctcttaacctctagctatttggttgggc-tacacttccctatgattttagatat---tttctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
||| | | ||| ||||| || ||| | | | || | | | | | | | | | || | | || | || || | | || |||| | | || || | || | |||| | | | | |||| || | | | | | |||| || || | |||| ||||||||||| |||||||| || || |||||||| || || ||||||||||| ||||||||||| |||||||||| || | ||||||||||| || || |
gtaggtttaaaaggatatggatcttatagagatatggatttaat-taaaaaaaaggcctgaaaatcagttgttaactggg-gatgccaaaaaaaaagggctttgattaa--tttgtctgttgattacagcatgtacttgcttctattgttagctaaaaatgtttaactttttggatttgg-gtctaaattcttctccagATGGATGGGTTTGACCAGACTGTGAATGTTAAGGTCATAATGGCAACTAATCGAGCAGACACTCTGGACCCTGCACTTCTTCGTCCTGGAAGACTCGACC
upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S79_171V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatctatgaaatgatatttatgttaggtgctgtgagtaggttgttactactattagtagttactaatttctgatgggctgctgtgaattagtttttgtttctcttaacctctagctatttggttgggctacacttccctatgattttagatattttctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
| || | | | ||| |||| ||| || | | | | | || | || |||| ||||| || || | || ||| || | | | |||||||||||||| || |||||||||||||| || || |||||||| || || |||| || ||| | ||||| ||| | |||| |||||| | || ||||
-------------------------------------------------------------------------------------aattttgctcatttttatcttttccttct-ctctctctctcgtttttgttttgttttg-ttttgtttatttacttaactctttattt------ttgctatggg-tgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAATCGAGCGGATACTCTTGACCCCGCTTTACTGCGACCTGGACGACTCGATC
upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatctatgaaatgatatttatgt-taggtgctgtgagtaggttgttactactattagtagttactaatttctgatgggctgctgtgaattagtttttgtttctcttaacctctagctatttggttgggctacacttccctatgattttagatattttctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
|||||| | | || || | | || | || | || | | | | || | || | | | | || | ||| ||||| | | || | || | | | | ||| | || || | || | || |||||| ||| | | ||||||||||||||||| |||||||| ||||||||||| || ||||| || ||| | ||||| ||| | ||||| ||| ||||||| |||||| | |||||||
----gtatgaagtctttttaatttctcagttttttgtctgaagagtccattcctcaaatggtgg---acctcctaggtg-----atagatca---tttatttctgtacagaactcggtagtct-tcagttcatttttctcgtcgaagtttggctgcttttcttacatt--tttaatgttctggt------tacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAACCGGGCAGATACTCTAGACCCCGCTTTGTTGCGACCTGGACGTCTTGATC
upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 3
gtatctatgaaatgatatttatgttaggtgctgtgagtaggttgttactactattagtagttactaatttctgatgggctgctgtgaattagtttttgtttctcttaacctctagctatttggttgggctacacttccctatgattttagatattttctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
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-----------------------------------------------------------------------------------------------------------------------------------------------gtaaaaggaaccgagtagagtaagccgctgacgtcct--tgtgcttctcagATGGATGGTTTCGATCAAACCGTGAATGTGAAGGTTATCATGGCTACAAACCGTGCGGACACTTTGGATCCCGCGCTCTTGCGTCCGGGAAGACTTGACA
upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ04233 (Selaginella moellendorffii), 3'ss of exon 3
gtatctatgaaatgatatttatgttaggtgctgtgagtaggttgttactactattagtagttactaatttctgatgggctgctgtgaattagtttttgtttctcttaacctctagctatttggttgggctacacttccctatgattttagatattttctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
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-----------------------------------------------------------------------------------------------------------------------------------------------gtaaaaggaaccaagtagagtaagccgctgacgtcct--tgtgcttctcagATGGATGGTTTCGATCAAACCGTGAATGTGAAGGTTATCATGGCTACAAACCGTGCGGACACTTTGGATCCCGCGCTCTTGCGTCCGGGAAGACTTGACAMapped 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|254324498|gb|GR833923.1|GR833923EST: GGAGCTGATAGAGAAGTACAGCGTTATCCTTATGGAACTTTTTGAATCAG ATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAAC
genomic: GGAGCTGATAGAGAAGTACAGCG-TATCCTTATGGAAC-TTTTGAATCAGgtatctatga ... ttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAAC
EST:
gi|193675358|gb|FK619120.1|FK619120EST: CTTTTGAATCAG ATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAAC
genomic: CTTTTGAATCAGgtatctatga ... ttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgattttagatattttctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
gtttaat putative branch site (score: 4)
ttacctgttcttttct CT-rich tract
ttttagatattttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctatgaaatgatatttatgttaggtgctgtgagtaggttgttactactattagtagttactaatttctgatgggctgctgtgaattagtttttgtttctcttaacctctagctatttggttgggctacacttccctatgattttagatattttctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG