Sequence
atgc intronic sequence ATGC exonic sequence...aagtttcaattgacttttttccaagcctattgggtttgtagtgctaaaagaattgatttatgtataactgctctaaccttggttttattgttatcatcagATCTACGATATATTTCAGCTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCCACAATGCCTCCTGAGGCCCTTGAGATCACCAGGAAGTTTATGA
Basic information
species | Glycine max |
transcript | GLYMA17G06110.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G06110.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G72730.1 (Arabidopsis thaliana), 3'ss of exon 4
aagtttcaattgactt--ttttccaagcctattgggtttgtagtgctaaaagaattgatttatgtataactgctctaaccttggttttattgttatcatcagATCTACGATATATTTCAGCTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCCACAATGCCTCCTGAGGCCCTTGAGATCACCAGGAAGTTTATGA
|||| | | || | | ||| | ||| ||| | || | | ||| | | || || ||| | | ||| ||| | |||||| ||||| || || ||||| ||||| || ||| |||| || || ||||||||||| ||||||||||| || |||||||||||||| |||||||| ||||
--gtttaatcttgtttaatctcccattcacattttctttttctctctgataaaatcaagtcat------ttgttctta---taatttgatt-tctctgtcagATATACGACATCTTCCAGCTTCTTCCTTCCAAGGTTCAGGTTGGTGTTTTCTCTGCTACAATGCCTCCCGAAGCCCTTGAGATCACAAGGAAGTTCATGA
upper sequence: GLYMA17G06110.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
aagtttcaattgacttttttccaagcctattgggtttgtagtgctaaaagaattgatttatgtataactgctctaaccttggttttattgttatcatcagATCTACGATATATTTCAGCTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCCACAATGCCTCCTGAGGCCCTTGAGATCACCAGGAAGTTTATGA
|||| | | || ||| ||| ||| | | | || || | || | | || | | ||| ||| || |||||||| || ||||| ||||| || ||| | |||||||| || ||||| |||||||| ||||||||||| || || | |||||||| || || || ||||
--gttt---gttatcttcttcaaagt---ttgaatctaccct-ctgtggttatct-ctgatattgacttggttttgtgttgttttctggtgaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA
upper sequence: GLYMA17G06110.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G13920.2 (Arabidopsis thaliana), 3'ss of exon 4
aagtttcaattgacttttttccaagcctattgggtttgtagtgctaaaagaattgatttatgtataactgctctaaccttggttttattgttatcatcagATCTACGATATATTTCAGCTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCCACAATGCCTCCTGAGGCCCTTGAGATCACCAGGAAGTTTATGA
|| | | |||| || | | | | | | | || || | || | | |||| | | || |||||| | |||||||| || ||||| ||||| |||||| | ||||| ||||| || || ||||| || |||||||| || || || ||||||||||| |||||||| ||||
------gtatgcaaatatttctcagtgtttcaattccattctcgttatagt-ttaacttgaatctcactggttt---ctgggtttttt---------cagATCTATGACATATTCCAGCTTCTTCCACCAAAGATCCAAGTTGGTGTGTTCTCCGCAACAATGCCACCAGAAGCTCTTGAGATCACAAGGAAGTTCATGA
upper sequence: GLYMA17G06110.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g01920.t01 (Vitis vinifera), 3'ss of exon 3
aagtttcaattgacttttttcca-agcctattgggtttgtagtgctaaaagaattgatttatgtata--actgctctaaccttggttttattgttatcatcagATCTACGATATATTTCAGCTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCCACAATGCCTCCTGAGGCCCTTGAGATCACCAGGAAGTTTATGA
|| || ||| | | | | | | || | || || | |||| |||| ||||| | || || || |||||||| ||||| || || || || ||||| || ||||||| ||||| ||||||||||||||||| || |||||||||||||| || |||||||||||||
-ttatttttttaactctgtgttgtattccaagaacctcaacaacctttcaactttaatgcgtttatatcactgttctaa--taaattagtttcttccttgcagATCTATGATATTTTCCAACTCCTGCCATCAAAAGTTCAAGTTGGAGTGTTCTCTGCCACAATGCCACCCGAGGCCCTTGAGATTACAAGGAAGTTTATGA
upper sequence: GLYMA17G06110.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S31_150V6.5 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------aagtttcaattgacttttttccaagcctattgggtttgtagtgct----aaaagaattgatttatgtataactgctctaacc---ttggttttattgttatcatcagATCTACGATATATTTCAGCTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCCACAATGCCTCCTGAGGCCCTTGAGATCACCAGGAAGTTTATGA
| ||||| | | | | | | | | | | || | ||| ||| || | | | ||||| ||| || | || ||||| || || || || ||||| |||||| ||| |||||||||| || || |||||||||||||| || || || |||||||||||||||||||| ||||
gtttgttcggagagtcctggaatggtagaagaaatttgtttttactcccaagaaaactaattgtttgtgtgactatttcagttctctaattatcctccttataagctatgagagatattgctcaacgctaacgaaattgattcgggcatcttctgcagATTTATGACATCTTCCAGCTTCTTCCACAGAAGCTTCAAGTGGGTGTGTTTTCTGCCACAATGCCACCCGAAGCGCTTGAGATCACCAGGAAGTTCATGA
upper sequence: GLYMA17G06110.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S383_1V6.3 (Physcomitrella patens), 3'ss of exon 3
aagtttcaattgacttttttccaagcctattgggtttgtagtgctaaaagaattgatttatgtataactgctctaaccttggttttattgttatcat---cagATCTACGATATATTTCAGCTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCCACAATGCCTCCTGAGGCCCTTGAGATCACCAGGAAGTTTATGA
|| | | || | | | | || || ||| | | | || || || || |||| | || | | ||||| ||||| || ||||||||||| || ||| |||||||||| ||||||||||| || ||||||||||| ||||| |||||||| |||||||| ||||
--gtgttgagtggtctgagtatgt-cgcactgttttgataggggtgttggtgactgttacggtgaaaaggccgcttacttgcagtgatgtccaatacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTCTCTGCTACCATGCCTCCTGAAGCCCTCGAGATCACAAGGAAGTTCATGAMapped 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|10234411|gb|BE803299.1|BE803299EST: TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTCAAGGATCAG ATCTACGATATATTTCAGCTGCTTCCATCTAAGATTCAAGTGGGAGTTTTC
genomic: TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTCAAGGATCAGgtaccttttc ... ttatcatcagATCTACGATATATTTCAGCTGCTTCCATCTAAGATTCAAGTGGGAGTTTTC
EST:
gi|208036098|gb|GD833047.1|GD833047EST: TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTCAAGGATCAG ATCTACGATATATTTCAGCTGCTTCCATCTAAGATTCAAGTGGGAGTTTTC
genomic: TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTCAAGGATCAGgtaccttttc ... ttatcatcagATCTACGATATATTTCAGCTGCTTCCATCTAAGATTCAAGTGGGAGTTTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaagaattgatttatgtataactgctctaaccttggttttattgttatcatcagATCTACGATATATTTCAGCTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCCACAATGCCTCCTGAGGCCCTTGAGATCACCAGGAAGTTTATGA
ctctaac putative branch site (score: 2)
aattgatttatgtata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagtttcaattgacttttttccaagcctattgggtttgtagtgctaaaagaattgatttatgtataactgctctaaccttggttttattgttatcatcagATCTACGATATATTTCAGCTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCCACAATGCCTCCTGAGGCCCTTGAGATCACCAGGAAGTTTATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - ccaagcc
- - - - - - - - - - - - - - - -gggtttg
- - - - - - - - - - - - - - - - - - - - - - -aaaagaa