Sequence
atgc intronic sequence ATGC exonic sequencegtaattgtttcattatttaaccccattactccaaaattatgttatgatgttttcttttgctagttgtcatgtaaaaggaagataaatgatttgacgcatttcttgcggattttcagATATTGAGATGTGGCCCCCCACCTATGAACAAGGCCATGGCTGCTCACCTTGAAGCCCTTGGATATGCTCCTGAGATGCAGTTCCAGTTCTGATTCTCTT
Basic information
species | Glycine max |
transcript | GLYMA19G29720.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G29720.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g40990.1 (Oryza sativa), 3'ss of exon 8
--------------------------gtaattgtttcattatttaaccccattactccaaaattatgttatgatgttttcttttgctagttgtcatgtaaaaggaagataaatgatttgacgcatttcttgcggat--tttcagATATTGAGATGTGGCCCCCCACCTATGAACAAGGCCATGGCTGCTCACCTTGAAGCCCTTGGATATGCTCCTGAGATGCAGTTCCAGTTCTGATTCTCTT
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gtaggtgtcacattgtgatgtcttctgtggtagcgtgccttctggaacttggaac-cgacaatt--gctaagagaatagttgaagtgtatt-ccatctaccaagcaggacatctgtgtgaca-atgtatggttgctcctttcagATATTGAGATGCGGACCTCCTCCCATGAACAAAGCCATGGCTGAACACCTGGAGAATCTTGGCTACACGAAGGAAATGCAGTTCCAATTCTAAGCCTCCA
upper sequence: GLYMA19G29720.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G133213_T01 (Zea mays), 3'ss of exon 8
gtaattgtttcattatttaaccccattactccaaaattatgttatgatgttttcttttgctagttgtcatgtaaaaggaagataaatgatttgacgcatttcttgcggattttcagATATTGAGATGTGGCCCCCCACCTATGAACAAGGCCATGGCTGCTCACCTTGAAGCCCTTGGATATGCTCCTGAGATGCAGTTCCAGTTCTGATTCTCTT
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--------gtgaatcttgagtcttatttttttttcagttcactatgaagatcgattgtg-tattctctattcttg-------tatctaacctgagatgtgtttaccta--tttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACAAAGGAGATGCAGTTCCAGTTCTAAGCAATGT
upper sequence: GLYMA19G29720.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G422581_T01 (Zea mays), 3'ss of exon 3
gtaattgtttcattatttaaccccattactccaaaattatgttatgatgttttcttttgctagttgtcatgtaaaaggaagataaatgatttgacgcatttcttgcggattttcagATATTGAGATGTGGCCCCCCACCTATGAACAAGGCCATGGCTGCTCACCTTGAAGCCCTTGGATATGCTCCTGAGATGCAGTTCCAGTTCTGATTCTCTT
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--------gtgaatcttgagtcttatttttttcagttcac--tatgaagatcgattgtg-tattctctattcttg-------tatctaacctgagatgtgtttaccta--tttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACAAAGGAGATGCAGTTCCAGTTCTAAGCAATGT
upper sequence: GLYMA19G29720.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G127972_T01 (Zea mays), 3'ss of exon 3
gtaattgtttcattatttaaccccattactccaaa-attatgttatgatgttttcttttgctagttgtcatgtaaaaggaagataaatgatttgacgcatttcttgcggattttcagATATTGAGATGTGGCCCCCCACCTATGAACAAGGCCATGGCTGCTCACCTTGAAGCCCTTGGATATGCTCCTGAGATGCAGTTCCAGTTCTGATTCTCTT
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--------gtgaatcttgagtcttattttttttttcagttcactatgaagatcgattgtg-tattctctattcttg-------tatctaacctgagatgtgtttaccta--tttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACAAAGGAGATGCAGTTCCAGTTCTAAGCAATGT
upper sequence: GLYMA19G29720.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G076206_T01 (Zea mays), 3'ss of exon 5
--gtaattgtttcattatttaaccccattactccaaaattatg-ttatgatgttttcttttgctagttgtcatgtaaaaggaagataaatgatttgacgcatttcttgcggattttcagATATTGAGATGTGGCCCCCCACCTATGAACAAGGCCATGGCTGCTCACCTTGAAGCCCTTGGATATGCTCCTGAGATGCAGTTCCAGTTCTGATTCTCTT
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gtgaatcaggcttattgccttttctt-tcagttcactatgaggattgtcatgatttctct-----attcttgtatgattgtatctaacctggaatcttacatgtgtttacctatttcagATCCTAAGGTGTGGTCCTCCTTCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACGAAGGAGATGCAGTTCCAGTTCTAAGCAACGC
upper sequence: GLYMA19G29720.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaattgtttcattatttaaccccattactccaaaattatgttatgatgttttcttttgctagttgtcatgtaaa--aggaagataaatgatttgacgcatttcttgcg---gattttcagATATTGAGATGTGGCCCCCCACCTATGAACAAGGCCATGGCTGCTCACCTTGAAGCCCTTGGATATGCTCCTGAGATGCAGTTCCAGTTCTGATTCTCTT
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---------------------tgcaagagaatgtaacattgataaacaattcatttttggtgaggagcatatggtttaagatggtgtgtcgatctaagtatggttcatgtttaaattgcagATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTTGAAGCTCTGGGATACTCTCCGGAGATGCAATTCCAGTTCTGATCTGAATMapped 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|51336831|gb|CO980697.1|CO980697EST: CAAAGGAGATGATTCAAACACATTGCCCTGCTCCAGCACAAGATATTAAG ATATTGAGATGTGGCCCCCCACCTATGAACAAGGCCATGGCTGCTCACCTT
genomic: CAAAGGAGATGATTCAAACACATTGCCCTGCTCCAGCACAAGATATTAAGgtaattgttt ... ggattttcagATATTGAGATGTGGCCCCCCACCTATGAACAAGGCCATGGCTGCTCACCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttgtcatgtaaaaggaagataaatgatttgacgcatttcttgcggattttcagATATTGAGATGTGGCCCCCCACCTATGAACAAGGCCATGGCTGCTCACCTTGAAGCCCTTGGATATGCTCCTGAGATGCAGTTCCAGTTCTGATTCTCTT
atttgac putative branch site (score: 4)
ttttc putative PPT
aagataaatgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgtttcattatttaaccccattactccaaaattatgttatgatgttttcttttgctagttgtcatgtaaaaggaagataaatgatttgacgcatttcttgcggattttcagATATTGAGATGTGGCCCCCCACCTATGAACAAGGCCATGGCTGCTCACCTTGAAGCCCTTGGATATGCTCCTGAGATGCAGTTCCAGTTCTGATTCTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG