Sequence
atgc intronic sequence ATGC exonic sequence...tatttgagtgttgctcctccaccataattggacaattaatgaaaagtacattttgatgtcagcttttgaggatattatttgctgttgcatctttttacagATACCCGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGAACTGCTATGCTTGGTGTGGGTGTTTCCTCCAGTAAAAACC
Basic information
species | Glycine max |
transcript | GLYMA08G43500.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G43500.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4
tatttgagtgttgctcctccaccataattggacaattaatgaaaa-gtacattttgatgtcagcttttgaggatattatttgctgttgcatctttttacagATACCCGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGAACTGCTATGCTTGGTGTGGGTGTTTCCTCCAGTAAAAACC
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-------------------------------gtaagtattcttcttatctatgctgctgt-aacttgtgatcacacaatactcatctgaaaacttt-gcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC
upper sequence: GLYMA08G43500.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G119773_T01 (Zea mays), 3'ss of exon 4
tatttgagtgttgctcctccaccataattggacaattaatgaaaagtacattttgatgtcagcttttgaggatattatttgctgttgcatctttttacagATACCCGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGAACTGCTATGCTTGGTGTGGGTGTTTCCTCCAGTAAAAACC
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-----gtgggtggtttctcccctttcctgctctaacttatctgcaaattgttatcatgt-accttatgagtgaaca------------------ttgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC
upper sequence: GLYMA08G43500.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 4
---tatttgagtgttgctcctccaccataattggacaattaatgaaaagt-acattttgatgtc---agcttttgaggatattatttgctgttgcatctttttacagATACCCGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGAACTGCTATGCTTGGTGTGGGTGTTTCCTCCAGTAAAAACC
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gtgagtctatgtattgtataaagcacataacaagttggttgatgaatgcttattgattgatccccaaagattctgaggaaacagtata-tattttgttctttttcagATACCTGGACTAGTCAATGTAGATTTTGCAGATGTGAAGGCAGTCATGAAAGATTCTGGAACTGCAATGCTCGGGGTAGGTGTTTCTTCCAGCAAAAACC
upper sequence: GLYMA08G43500.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 4
--tatttgagtgttgctcctccaccataattggacaattaatgaaaagtacattttgatgtcagcttttgaggatattatttgctgttgcatctttttacagATACCCGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGAACTGCTATGCTTGGTGTGGGTGTTTCCTCCAGTAAAAACC
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actgatttattatgatattttcctgattaatttccaat-actgaagtttat-ctttgctgttgatcctatataatttaaaatagcgtgtccttgttttgcagATACCCGGGCTGGTAAATGTTGATTTTGCAGATGTAAAGGCAGTCATGAAGGACTCTGGAACTGCAATGCTTGGAGTGGGGGTTTCTTCCAGCAAAAACCMapped 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|19348082|gb|BM892614.1|BM892614EST: CAGATGACGTTCTACGACAAGGAGTACAGGGAATATCAGACATCATAACA ATACCCGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAA
genomic: CAGATGACGTTCTACGACAAGGAGTACAGGGAATATCAGACATCATAACAgtgagttgat ... ctttttacagATACCCGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtacattttgatgtcagcttttgaggatattatttgctgttgcatctttttacagATACCCGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGAACTGCTATGCTTGGTGTGGGTGTTTCCTCCAGTAAAAACC
ttttgat putative branch site (score: 4)
catcttttt putative PPT
atattattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatttgagtgttgctcctccaccataattggacaattaatgaaaagtacattttgatgtcagcttttgaggatattatttgctgttgcatctttttacagATACCCGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGAACTGCTATGCTTGGTGTGGGTGTTTCCTCCAGTAAAAACC
- - tgagtgt
- - - - - - -ctcctcc
- - - - - - - - - - - - - - - - - - - - gaaaagta
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttgc