Sequence
atgc intronic sequence ATGC exonic sequencegtaaaggcatttgcttatattccattcattcttgtctttatttttcctcctttctcaatgtagatgaaattgaatttgttttgcataatgtcattatttcagGGCTGTGATTGTTTAGGCTATATCAAATACTTTGATGCGCATTTCACAAACTTCTATGGAGGTGTTGAAACAATTGAAAACTGTGTTTGTTTGCACGAAG
Basic information
species | Glycine max |
transcript | GLYMA08G38990.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 6
gtaaaggcatttgcttatattccattca-ttcttg-tctttatttttcctcctttctcaatgtagatgaaattgaatttgttttgcataatgtcattatttcagGGCTGTGATTGTTTAGGCTATATCAAATACTTTGATGCGCATTTCACAAACTTCTATGGAGGTGTTGAAACAATTGAAAACTGTGTTTGTTTGCACGAAG
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---------------gttattttattcagttcttgatgtgtatactttgacgttcaaaatttttctttgatttgactatgctctt--taacctttttgtg-cagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGCATGAGG
upper sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 6
--------gtaaaggcatttgcttatattccattcattcttgtctttatttttcctcctttctca----atgtagatgaaattgaatttgttttgc-------ataatgtcattat--ttcagGGCTGTGATTGTTTAGGCTATATCAAATACTTTGATGCGCATTTCACAAACTTCTATGGAGGTGTTGAAACAATTGAAAACTGTGTTTGTTTGCACGAAG
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gttagagtgcttactcctatgctgattttctttgtattactattgttgttgttatatattagttacatcaggctaatcataatgatttttttttttttttttggtcatgtctgtgtggtgcagGGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAATTTCACTGGTGGTATCGAAACAATTGAAAATTGTGTTTGCTTGCATGAAG
upper sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S178_54V6.1 (Physcomitrella patens), 3'ss of exon 7
gtaaaggcatttgctta-tattccattcattcttgtctttatttttcctcctttct---caatgtagatgaaattgaatttgttttgcataatgtcattatttcagGGCTGTGATTGTTTAGGCTATATCAAATACTTTGATGCGCATTTCACAAACTTCTATGGAGGTGTTGAAACAATTGAAAACTGTGTTTGTTTGCACGAAG
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----agtcaactacacaatattttaaagactagaacagttgacgtgaagattttttatgcaatggatttgttgaggagttgattatcactgaaaagatg--tgcagGGATGTGATTGTCTGGGCCTGATCAAGTATTTTGATGCCCATTTTACCAATTTCCATGGAGGAGTTGAAACAATCGAAAACTGTGTCTGCATGCATGAAG
upper sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S9_129V6.1 (Physcomitrella patens), 3'ss of exon 7
gtaaaggcatttgcttatattccattcattcttgtctttatttttcctcctttctcaatgtagatgaaat--tgaatttgttttgcataatgtcattatttcagGGCTGTGATTGTTTAGGCTATATCAAATACTTTGATGCGCATTTCACAAACTTCTATGGAGGTGTTGAAACAATTGAAAACTGTGTTTGTTTGCACGAAG
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atcagctgctcaactcacgggcaacttgaacttcactatgcgagttgagttctttcaaaggaacagacttgctgagttgtcattgcgtagagatgtg----cagGGTTGCGATTGTCTTGGCTTAATTAAGTACTTTGATGCACATTTTACCAACTTCCATGGAGGAGTTGAAACGATAGAAAACTGTATTTGCATGCACGAAG
upper sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S363_39V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaaaggcatttgcttatattccattcattcttgtctttatttttcctcctttctcaatgtagatgaaattg--aatttgttttgcataatgtcattatttcagGGCTGTGATTGTTTAGGCTATATCAAATACTTTGATGCGCATTTCACAAACTTCTATGGAGGTGTTGAAACAATTGAAAACTGTGTTTGTTTGCACGAAG
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-ttagagcagaacactgaagcccttacctttaagttactagaacacgtgagttga-aatg-aaatgaacatgttgatttgattatcattcaaaaggtgtg-cagGGGTGTGATTGTCTTGGTCTGATTAAATACTTTGATGCCCATTTTACAAACTTTCATGGAGGAGTTGAAACGATCGAAAACTGTGTCTGCATGCATGAAGMapped 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|193542102|gb|FK496214.1|FK496214EST: TTGATGCTGGGGAAGATGGCTTGGGTAAAAATTCTCATTCTCTGAAGAAG GGCTGTGATTGTTTAGGCTATATCAAATACTTTGATGCGCATTTCACAAAC
genomic: TTGATGCTGGGGAAGATGGCTTGGGTAAAAATTCTCATTCTCTGAAGAAGgtaaaggcat ... attatttcagGGCTGTGATTGTTTAGGCTATATCAAATACTTTGATGCGCATTTCACAAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctttctcaatgtagatgaaattgaatttgttttgcataatgtcattatttcagGGCTGTGATTGTTTAGGCTATATCAAATACTTTGATGCGCATTTCACAAACTTCTATGGAGGTGTTGAAACAATTGAAAACTGTGTTTGTTTGCACGAAG
ttatttc CT-rich tract
aaattgaatttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaggcatttgcttatattccattcattcttgtctttatttttcctcctttctcaatgtagatgaaattgaatttgttttgcataatgtcattatttcagGGCTGTGATTGTTTAGGCTATATCAAATACTTTGATGCGCATTTCACAAACTTCTATGGAGGTGTTGAAACAATTGAAAACTGTGTTTGTTTGCACGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG