Sequence
atgc intronic sequence ATGC exonic sequencegttttcattttctacttttttcgtttcgtcgtgttgaatgttgaatacgatgtttataatggtgattttgttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTT
Basic information
species | Glycine max |
transcript | GLYMA13G35580.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G35580.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0174g00190.t01 (Vitis vinifera), 3'ss of exon 3
------------gttttcattttctacttttttcgtttcgtcgtgttgaat-gttgaatacgatgtttataatg-gtgattttgttatc-tgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTT
|| | ||| | | || | || | || | ||| | | | | | || || || || | |||| ||| || || ||| || || || || |||||||||||||| |||| ||||| |||||||| || || |||||||| ||||| |||||||| || || |||
gtatagtattcctcttgccccttcaaatattgtggtagcctccttttggtttggttagctctattttgatggtgtgctatttgcaaatcgtgtagCGGGCAAGACAGACTATCGTGCCAGGATTCGCCTGATCAATCAAGACAAGAATAAGTACAACACTCCAAAATATCGATTTGTCGTGCGATTT
upper sequence: GLYMA13G35580.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0094g00870.t01 (Vitis vinifera), 3'ss of exon 2
------------gttttcattttctacttttttcgtttcgtcgtgttgaatgttgaatacgatgtttataatggtgatttt----gttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTT
||| || | | | | || | |||| | | ||| ||| | || | ||||| | |||| || ||| |||||||||| || || ||| | || |||||||| |||||||||| ||||||||||| ||||||||||||||||| || ||||| || || |||
gtattgtactacatttccaatgttcattcttatagttt--ttgggttttcgtttg--ttcgctttttatggatttaatttctaaaattgtctacagAGGGAAAGACTGACTACAGGGCTAGGATTCGCCTGATTAATCAAGACAAGAACAAGTATAACACTCCGAAATATCGCTTTGTTGTGCGATTT
upper sequence: GLYMA13G35580.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S38_329V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------------------------------------------------------------------gttttcattttctacttttttcgtttcgtcgtgttgaatgttgaatacgatgtttataatggtgattttgttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTT
|| || | || ||| | | | | ||||| | || | || | | | || || ||||| ||||| || ||||||||||||||||| |||||||| |||| || ||||| |||||||| || ||||| ||||| ||||| | ||| || || |||
gtgagtgggtttggtttgtgtttgggcatggattgttttgagtgacttgtttgtttttatctttagagtgtttggaattcaattttggttggaatggtggtgtgtttagattagggtttctg-gctctgggttgttgcgtttttcggagga-gctgagggtgatgtggttgttga-tgcagCCGGTAAAACCGATTACCGTGCGAGGATTCGTTTGACTACCCAGGATAAGAACAAGTACAACACCCCGAAGTACCGTTATGTCGTGCGATTT
upper sequence: GLYMA13G35580.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S364_3V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------------------------gttttcattttctacttttttcgtttcg----tcgtgttga-atgttgaatacgatgtttataatggtgattttgttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTT
| || || ||| |||||| | || || || | | | | || ||| || | ||||| || |||||||||||||| || ||||| || |||| | ||||||||||||||| || ||||| ||||| ||||| || || ||||| ||
gtgcggatttttttgtggcatttgtcaccctcactgtcgaagatccttgatcttgaatcttttctgtgtgtcgttggtacagagggttgtatcgctggggtttctcgttttaggttttctgctggtatttcttgttgcggatctgagattgtgtgcatggattatgcagCTGGTAAAACCGATTACCGGGCGAGGATCCGTTTGACCACTCAGGACAAGAACAAGTACAACACCCCGAAGTACCGTTTCGTCGTTCGTTTC
upper sequence: GLYMA13G35580.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ31187 (Selaginella moellendorffii), 3'ss of exon 2
gttttcattttctacttttttcgtttcgtcgtgttgaatgttgaatacgatgtttataatggtgattttgttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTT
| || || | | ||| | ||||| || || | | | | | | |||| |||||| || |||||||| || || || | || |||| |||||||||||||||||||| ||||| ||||| |||||||| || |||||||||
-----------------gtaacgatttggattcttggagcttgaa----at-ttcacatttctcttcgcttcatctctagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGAACAAATACAACACACCGAAGTACCGATTCGTCGTTCGCTTT
upper sequence: GLYMA13G35580.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ17161 (Selaginella moellendorffii), 3'ss of exon 2
gttttcattttctacttttttcgtttcgtcgtgttgaatgttgaatacgatgtttataatggtgattttgttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTT
| || || | | ||| | ||||| || || | | | | || | | |||||| || |||||||| || || || | || |||| |||||||||||||||||||| ||||| ||||| |||||||| || |||||||||
-----------------gtaacgatttggattcttggagcttgaa----at-ttcacatt--tctcttcgct--tcatagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGAACAAATACAACACACCGAAGTACCGATTCGTCGTTCGCTTTMapped 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|17022323|gb|BM093357.1|BM093357EST: ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAG AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAGgttttcattt ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST:
gi|193513631|gb|FK467861.1|FK467861EST: ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAG AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAGgttttcattt ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgtcgtgttgaatgttgaatacgatgtttataatggtgattttgttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTT
ttttgtt CT-rich tract
atgtttataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttcattttctacttttttcgtttcgtcgtgttgaatgttgaatacgatgtttataatggtgattttgttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC