Sequence
atgc intronic sequence ATGC exonic sequence...ttctcacagcttatcataatatattgaatattgattttgaagatgttagatatgtattttctttataggctttatttgctttcacttttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
Basic information
species | Glycine max |
transcript | GLYMA08G28890.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 2
---------------------------------------------------------------------------------------------ttctcacagctta----tcataatatattgaatattgattttgaagatgttagatatgtattttctttataggctttatttgctttcacttttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
||| | || | ||| | ||||| || | ||| | | ||| | || ||| | | | |||| || |||||||||||| ||||| || ||||||||||||||||||||||||||| | ||||| | ||||| || ||||||||||| ||||||||||| |||||||||
gtaagtggtaacttagtctgcagttttagacttacaaaaaccaaaagtttgtttgctcatttatttgcaaattctgttggaaaatatggtctggactcttaactcaagaaccattgggctctctatattc-ttctctcctcgttttgcttatgctttgctatctagcattaaaaacatatatgtttgcttattacagTGAAGGACTAGGGGAAGCATATGATGGAGATATTGCATTTGCAAGTTCACTGGAAGCATTTGGAGGGGGGCATAATGATCCAATCAGTGTTGCTTTTGGA
upper sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 2
ttctcacagcttatcataatatattga---atattgattttgaagatgttagatatgtattttctttataggctttatttgctttcacttttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
| || | | |||| | | ||||| | | | || | | | | | | || | ||| ||| || || | | ||| ||| |||||| | || || || |||||||||||||||||||||||||| | | ||||| ||||| || || || |||||||| || ||||| ||||||||
-cattgcattacacgcttatatttaaacccatatttactc-gtagttttctgccaacttgctgctatccaggacacattaatttacatatccct-tttttcagGGAAGGATTAGGAGAAGCTTATGATGGAGATATTGCATTTGCAAGCTCACTCGAAACATTTGGGGGAGGCCACAATGACCCTATAAGTGTTGCTTTTGGT
upper sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 2
------------------ttctcacagcttatcataatatattgaatattga---ttttgaagatgttagatatgtattttctttataggctttatttg---ctttcacttttgtactttc----cagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
|| | ||| ||| | || || ||| || || || | | | ||| | ||| ||| | | ||||| ||| |||||| ||| |||||||| ||||| || |||||||||||||||||||| ||||| | | ||||| ||||| || ||||||||||| ||||||||||| | ||||||
gtaagtgataatgtgtcatttacgtagcatatttgggt-taccaaaacctgaaagttctgtctctgatttgtgaaaagttttaattcagggtttctctatgcctttctaatttctacttttgtttcagGGAAGGACTAGGGGAAGCATATGATGGAGATATTGCATTCGCAAGCTCACTTGAAACATTTGGAGGGGGGCATAATGATCCAATCAGTGTCACATTTGGA
upper sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G872204_T02 (Zea mays), 3'ss of exon 2
--ttctcacagcttatcata-atatattgaatat-tgattttgaagatgttagatatgtattttctttataggctttatttgctttcacttttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
| || || || ||| | | | | || || ||| | || |||| | | | | || |||| | | || |||||||||||| ||||| || || |||||||||||||||||||| || | | ||||| ||||| || || || ||||| ||||| ||||| ||||||||
gtaagtaaccatccattgcccatgcatttattttgtaatccggagtatggttgagctgtaagtcactccctg-cgccatatgctgatatgcccttttgtttcagTGAAGGACTAGGGGAAGCATACGATGGAGATATTGCATTTGCCAGCTCACTTGAAACATTTGGAGGAGGCCACAATGATCCAATGAGTGTCGCTTTTGGT
upper sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------ttctcacagcttatcataat----atattgaatattgattttgaagatgttagatatgtattttctttataggctttatttgctttcacttttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
|| |||||||| || | || | || | || ||| || || | | | | |||| || || | | | || ||| |||||||||||| || ||||| || ||||| || ||||| || |||||||| | ||||| |||||||| || |||||||| ||||| |||||||||||||||
gtatgctagttcaaattttcacagctaattaggattgtagctctacatttagagttttcttctggctgaaacatgtatcttttaacagcgataga-----ttattctttctttttacagTGAAGGACTAGGCGAGGCATACGATGGGGACATTGCTTTCGCAAGTGCACTTGAAACATTTGGTGGAGGCCATAATGATCCAATAAGTGTGGCTTTTGGA
upper sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 2
ttctcacagcttatcataatatattgaatattgattttgaagatgttag-atat-gtattttctttataggctttatttgctttcacttttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
|| | | | | | | || || | | | | || | || | || | | || || || | ||| | || || | | || ||||||||| |||||||| | |||||||| || ||||| ||||||||||| | |||||||||||||| || || ||||| || || |||||||||||||||
ttgttattcagttttggtgtttcttatggatgaaatcaacatttctttccacatagcatgcttgtcat-ggtttcaattg-tctctgttctctgaattgcagTGAAGGGCTTGGGGAAGGATATGATGGGGACATTGCTTTTGCAAGTGCTCTAGAAACTTTTGGTGGAGGACACAATGATCCTATTAGTGTGGCTTTTGGA
upper sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ24732 (Selaginella moellendorffii), 3'ss of exon 2
ttctcacagcttatcataatatattgaatattgattttgaagatgttagatatgtattttctttataggctttatttgctttcacttttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
| | | ||| || || | ||| | || | | | | |||| || |||| | || |||||||||||| || || || || ||||||||||| || ||||| ||||| |||||||| |||||||| |||||| |||| || || || || ||| |||||
-------------------------gtaagcccactttaccgag--taattgtgttccatgttca-atccggtctttgtttctctttttttcct--acagTGAAGGACTCGGTGAAGCGTACGATGGAGATATCGCTTTTGCTAGTGCTTTGGAAACATTTGGTGGCGGGCATGATGATCCCATTAGCGTCGCTGTTGGA
upper sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ08060 (Selaginella moellendorffii), 3'ss of exon 2
ttctcacagcttatcataatatattgaatattgattttgaagatgttagatatgtattttctttataggctttatttgctttcacttttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
| | | | | || || | ||| | || | | | | |||| || |||| | || |||||||||||| || || || || ||||||||||| || ||||| ||||| |||||||| |||||||| |||||| |||| || || || || ||| |||||
-------------------------gtaagcccactctaccgag--taactgtgttccatgttca-atccggtctttgtttctctttttttcct--acagTGAAGGACTCGGTGAAGCGTACGATGGAGATATCGCTTTTGCCAGTGCTTTGGAAACATTTGGTGGCGGGCATGATGATCCCATTAGCGTCGCTGTTGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagatatgtattttctttataggctttatttgctttcacttttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
cttttgtactttcc CT-rich tract
tatgtattttctttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctcacagcttatcataatatattgaatattgattttgaagatgttagatatgtattttctttataggctttatttgctttcacttttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG