Sequence
atgc intronic sequence ATGC exonic sequencegtgcgttcaattaatcatcccattttattattaactttttttagtacgaaattatgtatatttatgttagcttgaaataaaattaatattgtacgcattgcatgcgcagGAAAAGAATAAGGGAGCGTTCGATTTCATCTATGTGGATGCTGATAAGGACAACTACTTGAACTACCACAAGAGGGTGATTGAGCTTGTGAAGGTTGGGG
Basic information
species | Glycine max |
transcript | GLYMA11G05800.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G05800.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0031g00350.t01 (Vitis vinifera), 3'ss of exon 4
gtgcgttcaattaatcatcccattttattattaactttttttagtacgaaattatgtatatttatgttagcttgaaataaaatt--aatattgtacgcattgcatgcgcagGAAAAGAATAAGGGAGCGTTCGATTTCATCTATGTGGATGCTGATAAGGACAACTACTTGAACTACCACAAGAGGGTGATTGAGCTTGTGAAGGTTGGGG
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-----------------gtaagtacaataatgcccctagcccactccaatattctccatgcctcatctgaacagaattgtaatttcaaaattat---caccaaat-tgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGACAACTACCTGAACTACCACAAAAGGCTGATTGATCTGGTCAAGGTTGGAG
upper sequence: GLYMA11G05800.2 (Glycine max), 3'ss of exon 4
lower sequence: EFJ22516 (Selaginella moellendorffii), 3'ss of exon 4
gtgcgttcaattaatcatcccattttattattaactttttttagtacgaaattatgtatatttatgttagcttgaaataaaattaatattgtacgcattgcatgcgcagGAAAAGAATAAGGGAGCGTTCGATTTCATCTATGTGGATGCTGATAAGGACAACTACTTGAACTACCACAAGAGGGTGATTGAGCTTGTGAAGGTTGGGG
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-----------------------------gtaagctttc---aatacaacttt-----tctttatcttaccttgaaccaacgacaatgctg---acactttcctcgcagGAGGCGAATCATGGCGCATTCGACTTCATCTTTGTGGATGCTGACAAGGACAATTACTTGAACTACCACAAGAGGTTGATCTCTTTGGTTAAAGTCGGAG
upper sequence: GLYMA11G05800.2 (Glycine max), 3'ss of exon 4
lower sequence: EFJ11728 (Selaginella moellendorffii), 3'ss of exon 4
gtgcgttcaattaatcatcccattttattattaactttttttagtacgaaattatgtatatttatgttagcttgaaataaaattaatattgtacgcattgcatgcgcagGAAAAGAATAAGGGAGCGTTCGATTTCATCTATGTGGATGCTGATAAGGACAACTACTTGAACTACCACAAGAGGGTGATTGAGCTTGTGAAGGTTGGGG
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-----------------------------gtaagctttc---aatacaacttt-----tctttatcttaccttgaaccaacgacaatgctg---acactttcctcgcagGAGGCGAATCATGGCGCGTTCGACTTCATCTTTGTGGATGCTGACAAGGACAATTACTTGAACTACCACAAGAGGTTGATCTCTTTGGTTAAAGTCGGAGMapped 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|192329245|gb|FK020164.1|FK020164EST: CTCATCAAAGAC GAAAAGAATAAGGGAGCGTTCGATTTTCATCTATGTGGATGCTGATAAGGA
genomic: CTCATCAAAGACgtgcgttcaa ... gcatgcgcagGAAAAGAATAAGGGAGCGTTCGA-TTTCATCTATGTGGATGCTGATAAGGA
EST:
gi|14991737|gb|BI317410.1|BI317410EST: ACTTCAGAGAAGGACCTGCTCTTCCTCTTCTTGATCAACTCATCAAAGAC GAAAAGAATAAGGGAGCGTTCGATTTCATCTATGTGGATGCTGATAAGGAC
genomic: ACTTCAGAGAAGGACCTGCTCTTCCTCTTCTTGATCAACTCATCAAAGACgtgcgttcaa ... gcatgcgcagGAAAAGAATAAGGGAGCGTTCGATTTCATCTATGTGGATGCTGATAAGGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtatatttatgttagcttgaaataaaattaatattgtacgcattgcatgcgcagGAAAAGAATAAGGGAGCGTTCGATTTCATCTATGTGGATGCTGATAAGGACAACTACTTGAACTACCACAAGAGGGTGATTGAGCTTGTGAAGGTTGGGG
aattaat putative branch site (score: 3)
atttatgttagcttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgttcaattaatcatcccattttattattaactttttttagtacgaaattatgtatatttatgttagcttgaaataaaattaatattgtacgcattgcatgcgcagGAAAAGAATAAGGGAGCGTTCGATTTCATCTATGTGGATGCTGATAAGGACAACTACTTGAACTACCACAAGAGGGTGATTGAGCTTGTGAAGGTTGGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT