Sequence
atgc intronic sequence ATGC exonic sequence...agaaaagaaaaaaatgtttaaaccgagactgatgtaatatatcattttgagagatatcttgatcttacagatacctaatcaaagtaaaattgttgtctagTTCTTGGAACCCCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGCGATCGTGCAATTGCCGATGGAAGCCTTCTAGATTTCTTGAGACAAGTCTCTA
Basic information
species | Glycine max |
transcript | GLYMA20G09810.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G09810.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 9
agaaaagaaaaaaatgtttaaaccgagactgatgtaatata-tcattttgagagatatcttgatcttacagatacctaatcaaagtaaaattgttgtctagTTCTTGGAACCCCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGCGATCGTGCAATTGCCGATGGAAGCCTTCTAGATTTCTTGAGACAAGTCTCTA
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-------------gtacataggctaagatacaaaaaacttgcttactatgctatacgttttggttgtcct----tctggttgaaggtttcttcttttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGGTCTCTCTGTGCCTGTGGTGATAATTCTATTGCAGATGGCAGTCTTCTTGACTTTCTACGGCAAGTGTCCA
upper sequence: GLYMA20G09810.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G473001_T01 (Zea mays), 3'ss of exon 7
agaaaagaaaaaaatgtttaaaccgagactgatgtaatatatcattttgagagatatcttgatcttacagatacctaatcaaagtaaaattgttgtctagTTCTTGGAACCCCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGCGATCGTGCAATTGCCGATGGAAGCCTTCTAGATTTCTTGAGACAAGTCTCTA
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---------gttgagaattaaccagtaat--attcagaaaataatattgatttttgtttttcctcagcgggt-tctgatagatgcca---tcttttgtagCTGTTGGAGCCCTTGGAACTATGTTACAGATCACTCTGTGCTTGTGGTGACTCTGTAATTGCTGATGGAACCCTTCTGGATTTCTTGCGTCAAGTGTCCA
upper sequence: GLYMA20G09810.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 7
agaaaagaaaaaaatgtttaaaccgagactgatgtaatatatcattttgagagatatcttgatcttacagatacctaatcaaagtaaaattgttgtct-----agTTCTTGGAACCCCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGCGATCGTGCAATTGCCGATGGAAGCCTTCTAGATTTCTTGAGACAAGTCTCTA
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--caggttgaaacataaccaagataaag--gatctttctaaccgttttgggatatattatg-ttttatggattctcgtctcgagtgagtcttttttctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA
upper sequence: GLYMA20G09810.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 7
agaaaagaaaaaaatgtttaaaccgagactgatgtaatatatcattttgagagatatcttgatc--tta-------cagatacctaatcaaagtaaaattgttgtctagTTCTTGGAACCCCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGCGATCGTGCAATTGCCGATGGAAGCCTTCTAGATTTCTTGAGACAAGTCTCTA
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---------cagattgcattttattaatctaccattttttttcctttttgcatagttcttgtctgtttagctggattaggtactgattgggaattatatttttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGACCGACCAATTGCTGATGGAAGCCTTCTCGATTTTCTGAGACAAGTGTCCAMapped 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|151396752|gb|EV266625.1|EV266625EST: GGATACTCTGACATTCCAGAGGAAGAGACTTTTACCAATGTTTGAGGGAG TTCTTGGAACCCCTTGAACTCTGTTACAGATCACTCTGTGCTTGTTGGCG
genomic: GGATACTCTGACATTCCAGAGGAAGAGACTTTTACCAATGTT-GAGG-AGgtacatattc ... tgttgtctagTTCTTGGAACCCCTTGAACTCTGTTACAGATCACTCTGTGCTTGT-GGCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgagagatatcttgatcttacagatacctaatcaaagtaaaattgttgtctagTTCTTGGAACCCCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGCGATCGTGCAATTGCCGATGGAAGCCTTCTAGATTTCTTGAGACAAGTCTCTA
acctaat putative branch site (score: 3)
taatcaaagtaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaaaagaaaaaaatgtttaaaccgagactgatgtaatatatcattttgagagatatcttgatcttacagatacctaatcaaagtaaaattgttgtctagTTCTTGGAACCCCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGCGATCGTGCAATTGCCGATGGAAGCCTTCTAGATTTCTTGAGACAAGTCTCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - -aaaaaaa
- - - - - - - - - - - - - -actgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagtaaaa