Sequence
atgc intronic sequence ATGC exonic sequencegtttgtatattttcaaaagtccttcttttcttctattattaactactgaattctatatttttaatgatctttcatgtttggatcatgtgacagGCTGAAGTGAATTTTCTCGGTGATCTAGTTCATCCAAACCTTGTTAAACTTGTAGGTTACTGCATTGAAGATGATCAAAGGTTGCTAGTGTATGAATTCA
Basic information
species | Glycine max |
transcript | GLYMA01G04930.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 2
gtttgtatattttcaaaag-tccttcttttcttctattattaactactgaattctatattttta-atgatctttcatgtttggatcatgtga----cagGCTGAAGTGAATTTTCTCGGTGATCTAGTTCATCCAAACCTTGTTAAACTTGTAGGTTACTGCATTGAAGATGATCAAAGGTTGCTAGTGTATGAATTCA
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----gtatgttttgaattgcttcagcatacagaccacaaaatattattcaactgtcttctaatgcatcatcaattaaactagcgttatttcattttcagGCAGAAGTTGATTTTCTTGGAAACCTTCAACATCCACACCTAGTGAAATTGGTTGGTTACTGCATCGAAGATGACCAAAGGTTGCTAGTGTATGAATTTA
upper sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 2
gtttgtatattttcaaaagtccttcttttcttctattattaactactgaattctatatttttaatg-atctttcatgtttggatcatg------tgacagGCTGAAGTGAATTTTCTCGGTGATCTAGTTCATCCAAACCTTGTTAAACTTGTAGGTTACTGCATTGAAGATGATCAAAGGTTGCTAGTGTATGAATTCA
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----gtatgtttttattttttgttggtatactttgttgaagagtattattcagctctctgctaatgcgtcactaagcaaagtatcattgcttgtttgcagGCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTGGTTGGCTACTGCATTGAAGATGACCAGAGGTTGCTTGTGTATGAATTTA
upper sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G150806_T01 (Zea mays), 3'ss of exon 2
------------------------gtttgtatattttca-aaagtccttcttttcttctattattaactactgaattctatatttttaatgatctttcatgtttggatcatgtgacagGCTGAAGTGAATTTTCTCGGTGATCTAGTTCATCCAAACCTTGTTAAACTTGTAGGTTACTGCATTGAAGATGATCAAAGGTTGCTAGTGTATGAATTCA
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gtatgtgctatgtttgttttacctatttgcaagttcacatatgatgtttacatatttttggtgtcaattcttgatggctgcgtctc--atactctgttttaattg-atcttttc-cagGCTGAAGTTGATTTTCTTGGAAATCTTCACCATCCCAATTTGGTCAAGTTGATTGGATATTGTGTTGAAGATGACCAAAGGTTGCTGGTGTATGAATTCA
upper sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------------------------------------------gtttgtatattttcaaaagtccttcttttcttctattattaactactgaattctatatttttaatgatc--tttcatgtttgga------------------tcatgtgacagGCTGAAGTGAATTTTCTCGGTGATCTAGTTCATCCAAACCTTGTTAAACTTGTAGGTTACTGCATTGAAGATGATCAAAGGTTGCTAGTGTATGAATTCA
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gtttgaaactttcctaatctattttatttcctatatggaattgaactcctttatttgttcttcccccactttgtgtttttcttcttttgtcttttgttttttgtttttgatttttgatttatctttttttagaaatcccttttatgtcttggctcttctcaagtttaatctcattttgcagGCTGAAGTGAATTTCCTTGGTGACCTCATTCATCCTAATCTGGTCAAACTGATTGGTTATTGCATTGAAGATGATCAAAGGTTGCTAGTTTATGAGTTTAMapped 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|15285775|gb|BI469666.1|BI469666EST: CTGTAAAAACCCTAAACCATGATGGGCTCCAGGGTCATAAAGAATGGCTG GCTGAAGTGAATTTTCTCGGTGATCTAGTTCATCCAAACCTTGTTAAACTT
genomic: CTGTAAAAACCCTAAACCATGATGGGCTCCAGGGTCATAAAGAATGGCTGgtttgtatat ... catgtgacagGCTGAAGTGAATTTTCTCGGTGATCTAGTTCATCCAAACCTTGTTAAACTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaactactgaattctatatttttaatgatctttcatgtttggatcatgtgacagGCTGAAGTGAATTTTCTCGGTGATCTAGTTCATCCAAACCTTGTTAAACTTGTAGGTTACTGCATTGAAGATGATCAAAGGTTGCTAGTGTATGAATTCA
aattctatatttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtatattttcaaaagtccttcttttcttctattattaactactgaattctatatttttaatgatctttcatgtttggatcatgtgacagGCTGAAGTGAATTTTCTCGGTGATCTAGTTCATCCAAACCTTGTTAAACTTGTAGGTTACTGCATTGAAGATGATCAAAGGTTGCTAGTGTATGAATTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG