Sequence
atgc intronic sequence ATGC exonic sequencegtatttattggttttgccactttatatttcatttttaatcttccttctgtaactgtatttggaagtggaagactttcttatccattgctgccttcttttgatctgattgtacagCCGGATTTAAATGTGAGGGAAAAAATACTGATTTTAATTGATACATGGCAAGAAGCTTTTGGGGGCTATGGAGTTTATCCTCAATACTATGCAGCATATA
Basic information
species | Glycine max |
transcript | GLYMA06G12570.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G12570.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g09329.2 (Oryza sativa), 3'ss of exon 4
gtatttattggttttgccactttatatttcatttttaatcttccttctgtaactgtatttggaagtggaagactttcttatccattgctgccttctt-ttgatctgattgtacagCCGGATTTAAATGTGAGGGAAAAAATACTGATTTTAATTGATACATGGCAAGAAGCTTTTGGGGGC---TATGGAGTTTATCCTCAATACTATGCAGCATATA
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---------ggaaaaggcaccacaagaccaa-----gaccaaccagccaagact-tattcctatagttcctacattcttatgcttctgtatttgattgccaatttatgatttcagCCAGATTTAAATGTTCGGGAGAAAATATTGAGTTTGATTGACACATGGCAAGTGGCTTTTGGAGGTGCATCTGGCAGATATCCCCAGTATCACGCTGCTT---
upper sequence: GLYMA06G12570.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G21380.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatttattggttttgccactttatatttcatttttaatcttccttctg-taactgtatttggaagtggaagactttcttatccattgctgccttcttttgatctgatt-gtacagCCGGATTTAAATGTGAGGGAAAAAATACTGATTTTAATTGATACATGGCAAGAAGCTTTTGGGGG---CTATGGAGTTTATCCTCAATACTATGCAGCATATA
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-----------------------gtttttgtttaccattctcttacctgcttgttatatttcaattctg----ttatccaatctgcttaacctggaaatttatcaaatttatacagCCAGACCTGACTGTGAGGGAGAAGATACTTAGTTTATTAGATACATGGCAAGAAGCTTTTGGTGGAAGCGGCGGAAGATTCCCTCAGTACTACAATGCCT---
upper sequence: GLYMA06G12570.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g01180.t01 (Vitis vinifera), 3'ss of exon 3
gtatttattggttttgccactttatatttcatttttaatcttccttctgtaactgtatttggaagtggaagactttcttatccattgctgccttcttttg-----atctgattgtacagCCGGATTTAAATGTGAGGGAAAAAATACTGATTTTAATTGATACATGGCAAGAAGCTTTTGGGGGCTAT---GGAGTTTATCCTCAATACTATGCAGCATATA
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-------------gtgcctaatttcatcctggctt--gttttatgtatatatatatatatcatggcttgttgttttcattctcatattagtttatttttatctatgttcaaatctgcagCCAGACTTGAATGTAAGGGAAAAGATTCTAATTTTGATAGATACGTGGCAAGAAGCTTTTGGGGGACCTAGGGGAAGATATCCCCAATACTATGCTGCAT---Mapped 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|192296865|gb|FG991906.1|FG991906EST: TCGTTGAGCGAGATATCTTACATGAAATGGTTAAGATAGTAAAGAAGAAG CCGGATTTAAATGTGAGGGAAAAAATACTGATTTTAATTGATACATGGCAA
genomic: TCGTTGAGCGAGATATCTTACATGAAATGGTTAAGATAGTAAAGAAGAAGgtatttattg ... gattgtacagCCGGATTTAAATGTGAGGGAAAAAATACTGATTTTAATTGATACATGGCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggaagtggaagactttcttatccattgctgccttcttttgatctgattgtacagCCGGATTTAAATGTGAGGGAAAAAATACTGATTTTAATTGATACATGGCAAGAAGCTTTTGGGGGCTATGGAGTTTATCCTCAATACTATGCAGCATATA
atctgat putative branch site (score: 4)
tttcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttattggttttgccactttatatttcatttttaatcttccttctgtaactgtatttggaagtggaagactttcttatccattgctgccttcttttgatctgattgtacagCCGGATTTAAATGTGAGGGAAAAAATACTGATTTTAATTGATACATGGCAAGAAGCTTTTGGGGGCTATGGAGTTTATCCTCAATACTATGCAGCATATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC