Sequence
atgc intronic sequence ATGC exonic sequence...ttacaattcatctggtggataggctatttgaggcaaataagttcagtcattccttcattctggaatcagttaatttactgaaattggcctcattttttagTTGGATCCGGAGCTGGAGTTTGATCGTGAAGTATACCCTTTGGGACTTCTTCCAAATGCTGGTGTGGTTGTTGGTGTTTCCCAGAGAATGTCATTTCCAG
Basic information
species | Glycine max |
transcript | GLYMA09G39270.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39270.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g54500.1 (Oryza sativa), 3'ss of exon 10
------------------------------------------------------------------tta-caattcatctggtggataggct--atttgaggca-aataagttcag---------tcattccttcatt---------ctggaatcagtt----aatttactgaaattggcctcatttttt-----agTTGGATCCGGAGCTGGAGTTTGATCGTGAAGTATACCCTTTGGGACTTCTTCCAAATGCTGGTGTGGTTGTTGGTGTTTCCCAGAGAATGTCATTTCCAG
||| ||||| | | | ||| | || || | || |||| |||| || ||| | |||| ||| ||| || ||| || | |||| || || ||||||||||||| || ||||| ||||| || || || | || ||||||||||||| |||||| ||||||||| |||| ||||||||||| || |
gtacagattttgtatcttgtgatagtattgacatctcttttgagttttgcgatccactctgtgaatttatcaattttttttggggaaaaacttgatcaaaatcataatagtttcatatgttgttttctttcttgcattgaactcttattggtggtagtattcaaagttaatggagaacatgctatttgtttctgcagCTGGATCCGGAGCTTGAATTTGACCGTGAGGTGTATCCGCTTGGTCTTCTTCCAAATGTTGGTGTAGTTGTTGGTATTTCTCAGAGAATGTCCTTCTCGA
upper sequence: GLYMA09G39270.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G475867_T01 (Zea mays), 3'ss of exon 10
-------------------------------------------------------ttacaattcatctg--gtggataggctatttgaggcaaataagttcagtcattccttcattctggaatcagt--taatt-tactga-aattggcc---tcattttttagTTGGATCCGGAGCTGGAGTTTGATCGTGAAGTATACCCTTTGGGACTTCTTCCAAATGCTGGTGTGGTTGTTGGTGTTTCCCAGAGAATGTCATTTCCAG
||| | | || || | | || || || || || ||| || || | | || || | | | | | | | || | |||||||| |||||||| |||||||||||||| || || ||| | || ||||||||||||| ||||||||||||||||||||| ||||||||||| || ||
gtataagtctctgccatgagataattatgaatatccattataagttttgttacctttatgagaaacttgctgtagtcataatactttcatattctattcctcttctttaattcgttgaagacctcatgatgatgatattaacagcttgtcatgttatactgtagTTGGACCCGGAGCTTGAGTTTGATCGTGAGGTGTATCCTCTTGGTCTTCTTCCAAATGTTGGTGTGGTTGTTGGTGTTTCTCAGAGAATGTCCTTCTCAA
upper sequence: GLYMA09G39270.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G052750_T02 (Zea mays), 3'ss of exon 10
ttacaattca-tctggtggataggctatttgaggcaaataagttcagtcattccttcattctggaatcagttaatt--tactgaaattggcctcattttttagTTGGATCCGGAGCTGGAGTTTGATCGTGAAGTATACCCTTTGGGACTTCTTCCAAATGCTGGTGTGGTTGTTGGTGTTTCCCAGAGAATGTCATTTCCAG
|| | || | | || | | | | || | | || ||| | | || | | ||| | || | || | | | || | ||| ||||||||||||| ||||||||||| || || || ||| | || ||||||||||| | ||||||||||||||||||||||||||| ||||| || ||
ctaaactttagtgaggggaaccaaacacctcct-taattcgttgaagacat--catgatgatattaacagccagttataaatgcatgtcatgtgatactgtagCTGGATCCGGAGCTTGAGTTTGATCGCGAGGTGTATCCTCTTGGTCTTCTTCCAAACGTTGGTGTGGTTGTTGGTGTTTCCCAGAGGATGTCCTTCTCAA
upper sequence: GLYMA09G39270.2 (Glycine max), 3'ss of exon 11
lower sequence: AT3G61480.1 (Arabidopsis thaliana), 3'ss of exon 11
------------------------------------------------------------------------ttacaat-tcatctggtggataggctatttgaggcaaataagttcagtcattccttcattctggaatcagtt--aatttactgaaattg-gcctcattttttagTTGGATCCGGAGCTGGAGTTTGATCGTGAAGTATACCCTTTGGGACTTCTTCCAAATGCTGGTGTGGTTGTTGGTGTTTCCCAGAGAATGTCATTTCCAG
| ||| | | | || | | ||| | || || | | | | | ||| | || || ||| | | ||| | |||| || || ||||||| ||| |||| ||||||||||| || || || ||||||||| | ||||| | || || |||||||| ||||| ||||||||||||||| | |
gtatgcatgctagtagagtccattttcaccgccattggtggcttatctttttgttctgatttttattgtctgtaacattattgtttgacgacattgacattcaaa-cacatccctcttataaatttctaattttttcattgtttcaaatgcatttttattatgttccattcttcagCTGGATCCAGAGTTGGAATTTGATCGTGAGGTGTATCCCTTGGGACTTTTACCAAACGTGGGCGTCGTTGTTGGAGTTTCTCAGAGAATGTCATTTTCGG
upper sequence: GLYMA09G39270.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv15s0046g01890.t01 (Vitis vinifera), 3'ss of exon 11
ttacaattcatctggtggataggctatttgaggcaaataagttca-gtcattccttcattctggaatcagttaat--ttactgaaattggcctcattttttagTTGGATCCGGAGCTGGAGTTTGATCGTGAAGTATACCCTTTGGGACTTCTTCCAAATGCTGGTGTGGTTGTTGGTGTTTCCCAGAGAATGTCATTTCCAG
|| |||| | ||| | ||| || | | || || | | ||| ||||| | || | || ||| | || ||| | | ||||||||||||| |||||||| ||||| ||||| |||||||| | || ||||||||||||||||| |||||||| |||||||||||||||||||||||| ||
-tagaattaaattggatggagtactagtt--agtagttatcttgatatgcttctttcatcgctgtattcctagatgcttaattaacttgacattgacatttagTTGGATCCTGAGCTGGAATTTGACCGTGAGATATACCCTCTTGGGCTTCTTCCAAATGCTGGGGTGGTTGTGGGTGTTTCCCAGAGAATGTCATTTACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcattccttcattctggaatcagttaatttactgaaattggcctcattttttagTTGGATCCGGAGCTGGAGTTTGATCGTGAAGTATACCCTTTGGGACTTCTTCCAAATGCTGGTGTGGTTGTTGGTGTTTCCCAGAGAATGTCATTTCCAG
agttaat putative branch site (score: 4)
cctcatttttt putative PPT
ttaatttactgaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttacaattcatctggtggataggctatttgaggcaaataagttcagtcattccttcattctggaatcagttaatttactgaaattggcctcattttttagTTGGATCCGGAGCTGGAGTTTGATCGTGAAGTATACCCTTTGGGACTTCTTCCAAATGCTGGTGTGGTTGTTGGTGTTTCCCAGAGAATGTCATTTCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- -caattca
- - - - - - tggtgga
- - - - - - - - - - - - - -ttgaggc