Sequence
atgc intronic sequence ATGC exonic sequence...taaaccaattattgttgctattggaagttttgaagctatagttcattttccatgtaatattttagtaataactaaaatctttctcttgcatgaacttaagGTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGACCGACTCAAGCCAGTGCTATACACAGAAGAAAGCTGCATTGTCCGGGAAG
Basic information
species | Glycine max |
transcript | GLYMA04G41610.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G41610.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g15580.1 (Oryza sativa), 3'ss of exon 5
taaaccaattattgttgctattggaagttttgaagctatagttcattttccatgtaatattttagt-aataactaaaatctttctcttgc--atgaacttaagGTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGACCGACTCAAGCCAGTGCTATACACAGAAGAAAGCTGCATTGTCCGGGAAG
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--ggtcattgatggct-taatacaaagattcctagttagctgataattaccggctatccctttagttaattaatcccttcattctttttctcaccatttgcagGTTCCAATGTTTGAAAACATGGATGAGAAGCTCTTGGATGCCATGTGTGATCGTCTAAAGCCCATGCTGTACACAGAAGGCAGCTGCATCATTCGCGAAG
upper sequence: GLYMA04G41610.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G148118_T02 (Zea mays), 3'ss of exon 6
-----taaaccaattattgttgctattggaagttttgaagctatagttcattttccatgtaatattttagtaataactaaaatctttctcttgcatgaacttaagGTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGACCGACTCAAGCCAGTGCTATACACAGAAGAAAGCTGCATTGTCCGGGAAG
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gattcaatattatatctttctcttaatgtcatgttttaatgaacagttgccgtagcttactatgttattagcatggttaaccttttgctgctgtttgca-----gGTTCCAATGTTTGAAAACATGGATGAACAGCTGTTGGATGCCATGTGTGATCGTCTAAAGCCTATGCTGTACACAGAAGGAAGCTGCATCATTCGCGAAG
upper sequence: GLYMA04G41610.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G129375_T01 (Zea mays), 3'ss of exon 1
-------------taaaccaattattgttgct--attggaagtt--ttgaagctatagttcattttccatgta---at--attttagtaataactaaaatctttctct-tgcatgaacttaagGTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGACCGACTCAAGCCAGTGCTATACACAGAAGAAAGCTGCATTGTCCGGGAAG
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gcatgttctcatctcccccttttatagtaccttgagttcagcctagcagaaactttttttttattttgatgtatgtattgatcttcctaattttttttaccttgctgtgttcatcgtttccagGTTCCACTGTTTGAAAATATGGACGAACAGCTTTTGGATGCCATGTGTGACTGCCTAAAGCCCATTCTGTACACAGAAGGTAGCTGCGTTATTCGCGAAG
upper sequence: GLYMA04G41610.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv16s0050g02560.t01 (Vitis vinifera), 3'ss of exon 7
taaaccaattattgttgctattggaagttttgaagct-atagttcattttccatgtaatatt--ttagtaata-actaaaatctttctcttgcatgaacttaagGTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGACCGACTCAAGCCAGTGCTATACACAGAAGAAAGCTGCATTGTCCGGGAAG
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----ttggttttcagcattgtgtgttgtcttcaagttgattggtaatgcaccattaattattactaaaccatggatttacatctttttcttaaacattgttaagGTGCCAATGTTCGAAAAGATGGATGAGCAACTGATGGATGCAATGTGTGACCGTCTCAAGCCAGCACTGTACACAGAAGATAGCTACATCGTCCGGGAGGMapped 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|298168849|gb|HO009779.1|HO009779EST: AGGGATATCAAGCGGCATCTTTGCCTGGCTTTGCTGACGAGG GTGCCGATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGAC
genomic: AGGGATATCAAGCGGCATCTTTGCCTGGCTTTGCTGATGAGGgtacgtttct ... tgaacttaagGTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttccatgtaatattttagtaataactaaaatctttctcttgcatgaacttaagGTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGACCGACTCAAGCCAGTGCTATACACAGAAGAAAGCTGCATTGTCCGGGAAG
tctttctcttgcat CT-rich tract
atgtaatattttagta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaaccaattattgttgctattggaagttttgaagctatagttcattttccatgtaatattttagtaataactaaaatctttctcttgcatgaacttaagGTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGACCGACTCAAGCCAGTGCTATACACAGAAGAAAGCTGCATTGTCCGGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC