Sequence
atgc intronic sequence ATGC exonic sequence...caattgctgcaatcagcttcctattgttgaaacttgaaaaccattcaaatgtgtagcatgtagtagcatccaatttacgttggtgtttggcattttacagGGTACAAGTAGACCAGCACACTATCACGTCCTCTGGGACGAGAACAATTTCACTGCAGATGAGATTCAGTCTCTAACCAACAATTTGTGCTACAC
Basic information
species | Glycine max |
transcript | GLYMA06G23920.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 19
caattgctgcaatcagcttcctat---tgttgaaacttgaaaaccattcaa-atgtgtagcatgtagtagcatccaatttacgttggtgtttggcattttacagGGTACAAGTAGACCAGCACACTATCACGTCCTCTGGGACGAGAACAATTTCACTGCAGATGAGATTCAGTCTCTAACCAACAATTTGTGCTACAC
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-acttggatcagcaaatattctgtctgtagtagcgctggaatataattccccaagtttgtcctccat--gtactgaaatgactgatgtgtgtga-gttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 19
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 18
caattgctgcaatcagcttcctattgttgaaacttgaaaaccattcaaatgtgtagcatgtagtagcatccaatttacgttgg--tgtttggcattttacagGGTACAAGTAGACCAGCACACTATCACGTCCTCTGGGACGAGAACAATTTCACTGCAGATGAGATTCAGTCTCTAACCAACAATTTGTGCTACAC
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ccttttaatcatgtgattgtacagccatggtacttgga--tcagtagcatgggaatatagtcagattctccgtactgtactgaaatgactgacgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 19
caattgctgcaatcagcttcctattgttgaaacttgaaaaccattcaaatgtg---tagcatgtagtagcatccaatttacgttggtgtttggcattttacagGGTACAAGTAGACCAGCACACTATCACGTCCTCTGGGACGAGAACAATTTCACTGCAGATGAGATTCAGTCTCTAACCAACAATTTGTGCTACAC
|| | | | | ||| || | | | ||| ||||| | ||| || | || ||| || ||| ||||| || ||||| || || ||||| || ||||||||||| |||||||||||||| ||||| || || ||| | | || ||||| | ||||||||
--atcatgtgattgtacagcttatggtacttggatcagtagcatgggaatgtagtcagactctccgtactatactggaatgactgatgtgtga-gtttgccagGGAACGAGTAGGCCTGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 19
lower sequence: EFJ19862 (Selaginella moellendorffii), 3'ss of exon 18
caattgctgcaatcagcttcctattgttgaaacttgaaaaccattcaaatgtgtagcatgtagtagcatccaatttacgttggtgtttggcattttacagGGTACAAGTAGACCAGCACACTATCACGTCCTCTGGGACGAGAACAATTTCACTGCAGATGAGATTCAGTCTCTAACCAACAATTTGTGCTACAC-----
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-------------------------------------gtaacatgatggcaccctggcctttgtagctttgctcatacgacgagact----atgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 19
lower sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 18
caattgctgcaatcagcttcctattgttgaaacttgaaaaccattcaaatgtgtagcatgtagtagcatccaatttacgttggtgtttggcattttacagGGTACAAGTAGACCAGCACACTATCACGTCCTCTGGGACGAGAACAATTTCACTGCAGATGAGATTCAGTCTCTAACCAACAATTTGTGCTACAC-----
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------------------------------------gtaacttgatggagccctggcct-ttgtagctttgctcatacgacgagact----atgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 19
lower sequence: EFJ14096 (Selaginella moellendorffii), 3'ss of exon 18
caattgctgcaatcagcttcctattgttgaaacttgaaaaccattcaaatgtgtagcatgtagtagcatccaatttacgttggtgtttggcattttacagGGTACAAGTAGACCAGCACACTATCACGTCCTCTGGGACGAGAACAATTTCACTGCAGATGAGATTCAGTCTCTAACCAACAATTTGTGCTACAC-----
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-----------------------------------gtaagttgatggagc-cctggcct-ttgtagctttgctcatacgacgagatt----atgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 19
lower sequence: EFJ19863 (Selaginella moellendorffii), 3'ss of exon 18
caattgctgcaatcagcttcctattgttgaaacttgaaaaccattcaaatgtgtagcatgtagtagcatccaatttacgttggtgtttggcattttacagGGTACAAGTAGACCAGCACACTATCACGTCCTCTGGGACGAGAACAATTTCACTGCAGATGAGATTCAGTCTCTAACCAACAATTTGTGCTACAC-----
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------------------------------------gtaacttgatggagccctggcct-ttgtagctttgctcatacgacgagact----atgttacagGGAACAAGCAGACCAGCACACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACGMapped 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|208092068|gb|GD890967.1|GD890967EST: GTCATCCTTCGGAATTCGACTTCTACTTGTGCAGTCATGCAGGAATTCAG GGTACAAGTAGACCAGACACACTATCACGTCCTCT
genomic: GTCATCCTTCGGAATTCGACTTCTACTTGTGCAGTCATGCAGGAATTCAGgtatgatcag ... cattttacagGGTACAAGTAGACCAG-CACACTATCACGTCCTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaatgtgtagcatgtagtagcatccaatttacgttggtgtttggcattttacagGGTACAAGTAGACCAGCACACTATCACGTCCTCTGGGACGAGAACAATTTCACTGCAGATGAGATTCAGTCTCTAACCAACAATTTGTGCTACAC
attttaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caattgctgcaatcagcttcctattgttgaaacttgaaaaccattcaaatgtgtagcatgtagtagcatccaatttacgttggtgtttggcattttacagGGTACAAGTAGACCAGCACACTATCACGTCCTCTGGGACGAGAACAATTTCACTGCAGATGAGATTCAGTCTCTAACCAACAATTTGTGCTACAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
caattgc
- - - -tgcaatc
- - - - - - - -gcttcct
- - - - - - - - - - - - tgttgaa
- - - - - - - - - - - - - - - - - - - - ccattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttggtg