Sequence
atgc intronic sequence ATGC exonic sequence...tatttgagtgaggtttctatgctatattttttgtttgatatgtagattgcatctgttgagttaattattttattgatgatttgttttctgttgctcacagGAAGAAGAAAGCTGTCCACAAGACTACTACTACAGATGACAAAAGGCTTCAAAGCACCCTGAAGAGGATAGGAGTGAATGCTATCCCTGCAATTGAAGAA
Basic information
species | Glycine max |
transcript | GLYMA01G18780.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G18780.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g01910.1 (Oryza sativa), 3'ss of exon 2
tatttgagtgaggtttctatgctatatttt--ttgtttgatatgtagattgcatctgttgagttaattattttattgatgatttgttttctgttgctcacagGAAGAAGAAAGCTGTCCACAAGACTACTACTACAGATGACAAAAGGCTTCAAAGCACCCTGAAGAGGATAGGAGTGAATGCTATCCCTGCAATTGAAGAA
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aagatatactgggcttgtattttgggatccgatcttttaaacaatgtattgtg-ctgtggcctttggattcatattaat-acttgttgtgcatttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG
upper sequence: GLYMA01G18780.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g34180.1 (Oryza sativa), 3'ss of exon 2
tatttgagtgaggtttctatgctatattttttgtttgatatgt-agattgcatctgttgagttaattattttattgatgatttgttttctgttgctcacagGAAGAAGAAAGCTGTCCACAAGACTACTACTACAGATGACAAAAGGCTTCAAAGCACCCTGAAGAGGATAGGAGTGAATGCTATCCCTGCAATTGAAGAA
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agaaaggatgtatattactcactactcactagtcatgatgtttcatactagtgctgttaggattctaattatgat-atgataagttttgtgttggtgacagAAAGAAGAAGGCAGTCCATAAGACTACAACCACAGATGACAAAAGACTTCAGAGCACTCTGAAAAGAGTAGGAGTAAACACCATCCCTGGCATTGAAGAG
upper sequence: GLYMA01G18780.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G131577_T03 (Zea mays), 3'ss of exon 2
--tatttgagtgaggtttctatgctatattttttgtttgatatgtagattgcatctgttgagttaattattttat-tgatgatttgttttctgttgctcacagGAAGAAGAAAGCTGTCCACAAGACTACTACTACAGATGACAAAAGGCTTCAAAGCACCCTGAAGAGGATAGGAGTGAATGCTATCCCTGCAATTGAAGAA
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gttatatatatatggtaccattgctgt--catatgtacggtaccggtctaggaagtcctggattcttacttataagttataactagctttg-gttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACGACCACAGATGATAAAAGGCTTCAGAGCACCCTGAAAAGAATAGGAGTGAACACCATTCCTGGTATTGAAGAG
upper sequence: GLYMA01G18780.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G001887_T03 (Zea mays), 3'ss of exon 2
-tatttgagtgaggtttctatgctatattttttgtttgatatgtagattgcatctgttgagttaattattttattgatgatttgttttctgttgctcacagGAAGAAGAAAGCTGTCCACAAGACTACTACTACAGATGACAAAAGGCTTCAAAGCACCCTGAAGAGGATAGGAGTGAATGCTATCCCTGCAATTGAAGAA
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gctgtcatatatggtaccaatgctgtcatacatatgataccggtccatgaaagtcctggattctgtacttataattataatt-atatttgattggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCAAAGCACCTTGAAAAGAATAGGAGTGAACAGCATTCCTGGTATTGAAGAGMapped 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|4395726|gb|AI494723.1|AI494723EST: AAGAAGATGGCCAGTTCTGTTCGAACTGGTGGGAAGGGTACTATGAGAAG GAAGAAGAAAGCTGTCCACAAGACTACTACTACAGATGACAAAAGGCTTCA
genomic: AAGAAGATGGCCAGTTCTGTTCGAACTGGTGGGAAGGGTACTATGAGAAGgtatatttgt ... ttgctcacagGAAGAAGAAAGCTGTCCACAAGACTACTACTACAGATGACAAAAGGCTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgcatctgttgagttaattattttattgatgatttgttttctgttgctcacagGAAGAAGAAAGCTGTCCACAAGACTACTACTACAGATGACAAAAGGCTTCAAAGCACCCTGAAGAGGATAGGAGTGAATGCTATCCCTGCAATTGAAGAA
tattgat putative branch site (score: 3)
ttttctgtt putative PPT
agttaattattttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatttgagtgaggtttctatgctatattttttgtttgatatgtagattgcatctgttgagttaattattttattgatgatttgttttctgttgctcacagGAAGAAGAAAGCTGTCCACAAGACTACTACTACAGATGACAAAAGGCTTCAAAGCACCCTGAAGAGGATAGGAGTGAATGCTATCCCTGCAATTGAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - tgagtga
- - - - - - - - ctatgct
- - - - - - - - - - - - - - - - - -tgatatg
- - - - - - - - - - - - - - - - - - - - - - - - gcatctg