Sequence
atgc intronic sequence ATGC exonic sequence...tctatgtttttaatcatctacttcaaccctttttgttatcattatcattaccatttttgaaagagaatgcacagttatatttcttaatctgttgttatagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAG
Basic information
species | Glycine max |
transcript | GLYMA09G03660.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G03660.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 5
tctatgtttttaatcatctacttcaaccctttttgttatcattatcattaccatttttgaaagagaatgcacagttatatttcttaatctgttgtt--atagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAG
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---------------gtaagtttgaaagcaatat----tccttgatctggtccatctggaatgtatacaaactgacatactgttttctctgtctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG
upper sequence: GLYMA09G03660.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G862107_T01 (Zea mays), 3'ss of exon 5
tctatgtttttaatcatctacttcaaccctttttgttatcattatcattaccatttttgaaagagaatgcacagttatatttcttaatctgttgttatagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAG
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---------gtaagaataaacaaaagcaacattttctcatgtgctgaatatgctttaggtaagcaactgacatatggtttcttttgctcaaat----tagGCTGATGAGATGGCTCAGATATTCAGGCAGAGAATAGCTCAGGCAGAGGCTATGGCTCGTGCTGACATGTTGAGATTCCAGCCAGAG
upper sequence: GLYMA09G03660.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G30510.1 (Arabidopsis thaliana), 3'ss of exon 5
tctatgtttttaatcatctacttcaaccctttttgttatcattatcattaccatttttgaaagagaatgcacagttatatttcttaatctgttgttata-gGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAG
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----------------gtaactctatttccattcaaaaaaactttccctattttcttttatgt------ctcaatcatttgctactttctgctgtctcaagGCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAG
upper sequence: GLYMA09G03660.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0077g00450.t01 (Vitis vinifera), 3'ss of exon 5
-tctatgtttttaatcatctacttcaaccctttttgttatcattatcattaccatttttgaa---agagaatgcacagt-tatatttcttaatc-tgttgttatagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAG
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ttctgttacttcacctataaaccaca--catgtgtgttgct----cctctacctatttgaaatccagtgatttaacaatacttggctcttaaccctgttctaacagGCGGAGGAGATGGCTCAGACATTCAGGCAGAGAATAGCTCAAGCAGAAGCTATGGCTCGGGCAGACATGCTAAGATTCCAACCTGAGMapped 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|11412222|gb|BF424233.1|BF424233EST: AACCCACACCTGGTGACATGATTCGCAATCCAAAGCTTGTCTTTGAGAAG GCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCT
genomic: AACCCACACCTGGTGACATGATTCGCAATCCAAAGCTTGTCTTTGAGAAGgtataattca ... gttgttatagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattaccatttttgaaagagaatgcacagttatatttcttaatctgttgttatagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAG
tcttaat putative branch site (score: 3)
agttatatttcttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctatgtttttaatcatctacttcaaccctttttgttatcattatcattaccatttttgaaagagaatgcacagttatatttcttaatctgttgttatagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - tcaaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgca