Sequence
atgc intronic sequence ATGC exonic sequence...ctctattatggctctatctctagccaaagtgacacttgggttttttccaatgcaaatcaacccatgtttcaattacagaataaaataattatgttttcagATACGCCAACAAAGTTCACATTTCTTGAGGGGATTTCAGCAACTTATGCAGAAGGATTGGATTGACATGTTTAATGAACATGAACTTCAG
Basic information
species | Glycine max |
transcript | GLYMA17G04180.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G04180.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G034622_T01 (Zea mays), 3'ss of exon 5
ctctattatggctctatctctagccaaagtgacacttgggttttttccaatgcaaatcaacccatgtttcaattacagaataaaataattatgttttcagATACGCCAACAAAGTTCACATTTCTTGAGGGGATTTCAGCAACTTATGCAGAAGGATTGGATTGACATGTTTAATGAACATGAACTTCAG
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-------------------gtaaaaagacagtagtcaatattcatatcattggatgcattaggaggctttgctaaatgttttcctggtttctatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAGCAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG
upper sequence: GLYMA17G04180.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G095887_T02 (Zea mays), 3'ss of exon 1
ctctattatggctctatctctagccaaagtgacacttgggttttttccaatgcaaatcaacccatgtttcaattacagaataaaataattatgttttcagATACGCCAACAAAGTTCACATTTCTTGAGGGGATTTCAGCAACTTATGCAGAAGGATTGGATTGACATGTTTAATGAACATGAACTTCAG
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-----------------gtaaaaagaaagtagtcaatagtcatatcattggatgcattagg--aggctttgctaaatgttttcctggtttctatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG
upper sequence: GLYMA17G04180.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G101098_T01 (Zea mays), 3'ss of exon 5
ctctattatggctctatctctagccaaagtgacacttgggttttttccaatgcaaatcaacccatgtttcaattacagaataaaataattatgttttcagATACGCCAACAAAGTTCACATTTCTTGAGGGGATTTCAGCAACTTATGCAGAAGGATTGGATTGACATGTTTAATGAACATGAACTTCAG
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-----------------------gtaaaaaga---ttgtagtcatatcatttggatgcattggaaggctttgctaattgttttcctggtttctatcatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCAAAAGACTGGATTGATATGTTCAATGAACATGAAATTCAG
upper sequence: GLYMA17G04180.1 (Glycine max), 3'ss of exon 20
lower sequence: AT3G17205.2 (Arabidopsis thaliana), 3'ss of exon 20
ctctattatggctctatctctagccaaagtgacacttgggttttttccaatgcaaatcaacccatgtttcaattacagaataaaataattatgttttcagATACGCCAACAAAGTTCACATTTCTTGAGGGGATTTCAGCAACTTATGCAGAAGGATTGGATTGACATGTTTAATGAACATGAACTTCAG
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--gtactggggaaccacttacctctcatttatc--ttggcatacctg------aggtcaccctgtaaatcaacagct-attgatatcatctcatttgcagATACGCCAGCAGAGTTCTCATTTCTTGAGGGGGTTTCAGCAACTCATTCCGAAAGAATGGATCGACATGTTCAATGAACATGAGCTTCAG
upper sequence: GLYMA17G04180.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv05s0077g00470.t01 (Vitis vinifera), 3'ss of exon 21
ctctattatggctctatctctagccaaagtgacacttgggttttttccaatgcaaatcaacccatgtttcaattacagaataaaataattatgttttcagATACGCCAACAAAGTTCACATTTCTTGAGGGGATTTCAGCAACTTATGCAGAAGGATTGGATTGACATGTTTAATGAACATGAACTTCAG
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--gtgagatcgcctttttcatagttaattc----cttcaaactcttcc--------ttgaactgttgcttgacgctaatatcaaataacatcactttcagATACGTCAGCAAAGTACTCATTTCTTGAGGGGTTTTCAGCAACTTATACAAAGAGATTGGATTGAAATGTTTGATGAGCATGAACTTCAGMapped 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|27425262|gb|CA936782.1|CA936782EST: ATGTCATTACTTTTATCCACCTTGTAGCCAATCACCGCTTGAATTTTCAG ATACGCCAACAAAGTTCACATTTCTTGAGGGGATTTCAGCAACTTATGCAG
genomic: ATGTCATTACTTTTATCCACCTTGTAGCCAATCACCGCTTGAATTTTCAGgtaaagttgc ... atgttttcagATACGCCAACAAAGTTCACATTTCTTGAGGGGATTTCAGCAACTTATGCAG
EST:
gi|151406815|gb|EV276630.1|EV276630EST: ATGTCATTACTTTTATCCACCTTGTAGCCAATCACCGCTTGAATTTTCAG ATACGCCAACAAAGTTCACATTTCTTGAGGGGATTTCAGCAACTTATGCAG
genomic: ATGTCATTACTTTTATCCACCTTGTAGCCAATCACCGCTTGAATTTTCAGgtaaagttgc ... atgttttcagATACGCCAACAAAGTTCACATTTCTTGAGGGGATTTCAGCAACTTATGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccaatgcaaatcaacccatgtttcaattacagaataaaataattatgttttcagATACGCCAACAAAGTTCACATTTCTTGAGGGGATTTCAGCAACTTATGCAGAAGGATTGGATTGACATGTTTAATGAACATGAACTTCAG
tgttttc CT-rich tract
atgtttcaattacaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctctattatggctctatctctagccaaagtgacacttgggttttttccaatgcaaatcaacccatgtttcaattacagaataaaataattatgttttcagATACGCCAACAAAGTTCACATTTCTTGAGGGGATTTCAGCAACTTATGCAGAAGGATTGGATTGACATGTTTAATGAACATGAACTTCAG
- - - - - - - - - - - - - - -tgacact
- - - - - - - - - - - - - - - - - - - - - - - - aatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa