Sequence
atgc intronic sequence ATGC exonic sequence...tttgggtgttgggcacttgagcctaaagcttttttttctttttagagaataaatctatacatgtatatttgtatttaataaaattatgcttccttgtcagTATGTGATCCAGTGATGGGTGATGAAGGAAAGCTTTATGTTCCTCAAGAGCTAGTATCAGTCTATCGTGAGAAG
Basic information
species | Glycine max |
transcript | GLYMA11G33970.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G33970.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G069758_T02 (Zea mays), 3'ss of exon 6
------------------------------------------tttgggtgttgggcacttgagcctaaagcttttttttctttttagagaataaatctatacatgta-tatttgtatttaataaaattatgcttccttgtcagTATGTGATCCAGTGATGGGTGATGAAGGAAAGCTTTATGTTCCTCAAGAGCTAGTATCAGTCTATCGTGAGAAG
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gtaatcttttctcatcttttgttatttgtatgcttgcttcttctttaataaatttaatttaacagggacaatttaggtcatagctagagactgactagacatggttaattcttctgtttgctaattgcaaacatgctg--cagTTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGCTAATATCTGTTTATCAACAGAAG
upper sequence: GLYMA11G33970.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G37850.2 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------------------------------------------------------------tttgggtgttgggcacttgagcctaaagcttttttttctttttagagaataaatctatacatgtatatttgta----tttaataaaattatgct--tccttgtcagTATGTGATCCAGTGATGGGTGATGAAGGAAAGCTTTATGTTCCTCAAGAGCTAGTATCAGTCTATCGTGAGAAG
||| | || | ||| || | | || | | || | || || | | | | | | | ||| | | ||| ||| || |||| | |||||||||||| ||||||||||||||||||||| | ||||| ||| |||| || ||| || |||||||| |||
gtgggtgcattgcgtcctctttttagtccctttatgtttttgataccttggaagattggaatagactctatctttgtagtatttttagttgcagaaaactggattgagaggtcattatctgttatgtgaacatgt-tttggatctctgaaatggtaaaattatgctaattttagtctattcctgattagTATGTGATCCGGTGATGGGTGATGAAGGAAAGTTGTATGTGCCTGAAGAACTGGTACATGTTTATCGTGAAAAG
upper sequence: GLYMA11G33970.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G37850.3 (Arabidopsis thaliana), 3'ss of exon 4
tttgggtgttgggcacttgagcctaaagcttttttttctttttagagaataaatctatacatgtatatttgta----tttaataaaattatgct--tccttgtcagTATGTGATCCAGTGATGGGTGATGAAGGAAAGCTTTATGTTCCTCAAGAGCTAGTATCAGTCTATCGTGAGAAG
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-----ttgcagaaaactggattgagaggtcattatctgttatgtgaacatgt-tttggatctctgaaatggtaaaattatgctaattttagtctattcctgattagTATGTGATCCGGTGATGGGTGATGAAGGAAAGTTGTATGTGCCTGAAGAACTGGTACATGTTTATCGTGAAAAG
upper sequence: GLYMA11G33970.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0006g01660.t01 (Vitis vinifera), 3'ss of exon 5
tttgggtgttgggcacttgagcc-taaagcttttttttctttttagagaataaatctatacatgtatatttgtatttaataaaattatgcttccttgtcagTATGTGATCCAGTGATGGGTGATGAAGGAAAGCTTTATGTTCCTCAAGAGCTAGTATCAGTCTATCGTGAGAAG
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-gaacatttttacttcttatattattctgcctactcttctcatcatatccaaaaataatgcctaatcatctcttctcattaatattggggcttttatcaagTTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGTTAGTGGCAATCTACCGTGAGAAGMapped 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|58016835|gb|CX703577.1|CX703577EST: ATTGCAAGTTGTCAACAAACTTCGGTCAACAAACCCAGGTCTTACATATG TATGTGATCCAGTGATGGGTGATGAAGGAAAGCTTTATGTTCCTCAAGAGC
genomic: ATTGCAAGTTGTCAACAAACTTCGGTCAACAAACCCAGGTCTTACATATGgtgagaatat ... tccttgtcagTATGTGATCCAGTGATGGGTGATGAAGGAAAGCTTTATGTTCCTCAAGAGC
EST:
gi|58023232|gb|CX709973.1|CX709973EST: ATTGCAAGTTGTCAACAAACTTCGGTCAACAAACCCAGGTCTTACATATG TATGTGATCCAGTGATGGGTGATGAAGGAAAGCTTTATGTTCCTCAAGAGC
genomic: ATTGCAAGTTGTCAACAAACTTCGGTCAACAAACCCAGGTCTTACATATGgtgagaatat ... tccttgtcagTATGTGATCCAGTGATGGGTGATGAAGGAAAGCTTTATGTTCCTCAAGAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaataaatctatacatgtatatttgtatttaataaaattatgcttccttgtcagTATGTGATCCAGTGATGGGTGATGAAGGAAAGCTTTATGTTCCTCAAGAGCTAGTATCAGTCTATCGTGAGAAG
atttaat putative branch site (score: 4)
cttccttgtc putative PPT
aaatctatacatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgggtgttgggcacttgagcctaaagcttttttttctttttagagaataaatctatacatgtatatttgtatttaataaaattatgcttccttgtcagTATGTGATCCAGTGATGGGTGATGAAGGAAAGCTTTATGTTCCTCAAGAGCTAGTATCAGTCTATCGTGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT