Sequence
atgc intronic sequence ATGC exonic sequencegtattttagaatttgacgtttccttctttctgagatttatgtattacttcattttaaaacttttcaattctgagttgagtcctgtccattgccgtttcttcatcgcttgcaaaattttagGTTCAAATCATTCGACAAGGATATCTTTCTAAACGATCCTCCAATTTGAGAGGTGACTGGAAAAGAAGGTATTTTGTTGTTGACAGTCGAGGAATGTTGT
Basic information
species | Glycine max |
transcript | GLYMA05G38550.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G38550.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
gtattttagaatttgacgtttccttctttctgagatttatgtattacttcattttaaaacttttcaattctgagttgagtcctg---tccattgccgtttcttcatcgcttgcaaaattttagGTTCAAATCATTCGACAAGGATATCTTTCTAAACGATCCTCCAATTTGAGAGGTGACTGGAAAAGAAGGTATTTTGTTGTTGACAGTCGAGGAATGTTGT
| || || | | ||| | ||| || | | | | | || | || | || || | | ||| | || | | | | | | ||| |||| || | |||||||||||| ||||| || || ||||| || || ||||||||||||||||||||||||| |||||| |||| || ||||||||||| |
----------gtagcacattctggttgtcctggaagtta-atactcttgcttatgtctacgctcaggctcacatttcagcatggaaattcatgtcatattttaaagtgagtactta-tttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT
upper sequence: GLYMA05G38550.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 11
gtattttagaatttgacgtttccttctttctgagatttatgtattacttcattttaaaacttttcaattctgagttgagtcctgtccattgccgtttcttcatcgcttgcaaaattttagGTTCAAATCATTCGACAAGGATATCTTTCTAAACGATCCTCCAATTTGAGAGGTGACTGGAAAAGAAGGTATTTTGTTGTTGACAGTCGAGGAATGTTGT
| | | | |||| | || || | | | || | || | || || | | | | | || |||| || | |||||| ||||| || || || ||| |||| || || ||||||| ||| ||||||||||||| |||||| |||| |||||||||||| |||
---------------------------------gtaccacttcctggttcactaggaa---ttaaagcttcatgcagacattctagtactgtcattcctgaaacaaa-gtatatgttcagGTCCAGACCATTCGTCAAGGTTACCTCTCGAAAAGATCTTCAAACTTGAGAGCTGATTGGAAAAGAAGGTTTTTTGTCCTTGATAGTCGAGGAATGCTGT
upper sequence: GLYMA05G38550.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 11
gtattttagaatttgacgtttccttctttctgagatttatgtattacttcattttaaaacttttcaattctgagttgagtcctgtccattgccgtttcttcatcgcttgcaaaattttagGTTCAAATCATTCGACAAGGATATCTTTCTAAACGATCCTCCAATTTGAGAGGTGACTGGAAAAGAAGGTATTTTGTTGTTGACAGTCGAGGAATGTTGT
| || | ||| ||| || | | ||| || || || || || | ||| | | | | | | | ||| ||||||| | |||||| ||||| ||||| ||||| |||| || || ||||||||||| |||||||| |||| ||||| | |||||||||||||||||||
-----------tgctggaactctccaaagacaatattcatgcat-gcatgattaagtaatttcataa----aagaagatgcatgttttatactgaaacgtaaggaactat----tttcagGTTCAGACCATTCGCCAAGGCTATCTATCTAAGAGATCTTCAAACTTGAGAGGTGATTGGAAAAGGAGGTTCTTTGTCCTCGACAGTCGAGGAATGTTGT
upper sequence: GLYMA05G38550.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G872204_T01 (Zea mays), 3'ss of exon 8
gtattttagaatttgacgtttccttctttctgagatttatgtattacttcattttaaaacttttcaattctgagttg-agtcctgtccattgccgtttcttcatcgcttgcaaaattttagGTTCAAATCATTCGACAAGGATATCTTTCTAAACGATCCTCCAATTTGAGAGGTGACTGGAAAAGAAGGTATTTTGTTGTTGACAGTCGAGGAATGTTGT
| ||| || | | | | | | ||| | | || ||| | ||| | | | | | || |||| | | ||| || ||||| |||||||| ||| |||| || || ||||||| |||||||||||||||| || || |||| |||||||||||| |||
-----------------------------gtaagacaccgatagtccaatacactggagatc--caaagcaggtttacagtttgaaaaaaaaaagttaaatggtgatgtactac-ttccagGTAGAGACCATCCGTCAAGGTTATCTTTCGAAAAGATCTTCAAACTTGAGAGCCGACTGGAAAAGAAGGTTCTTCGTACTTGATAGTCGAGGAATGCTGT
upper sequence: GLYMA05G38550.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G61980.1 (Arabidopsis thaliana), 3'ss of exon 11
gtattttagaatttgacgtttccttctttctgagatttatgtattacttcattttaaaacttttcaattctgagttgagtcctgtccattgccgtttcttcatcgcttgcaaaattttagGTTCAAATCATTCGACAAGGATATCTTTCTAAACGATCCTCCAATTTGAGAGGTGACTGGAAAAGAAGGTATTTTGTTGTTGACAGTCGAGGAATGTTGT
|| | || || | |||| ||| | | | | | | ||| | ||| ||| | | | || | ||| | | | || || ||||||| | || ||||||| ||||| |||||||| ||||| || ||||||||||||||||||||||| | ||| | |||| || || || ||| | |
---------gtaaggaaatatcttttgtattgaggcttactcgtcaaactgctgtcacatctttatactctc--ttgttttatatttat--ctgttgatataactgtt------cttcagGTTCAGACTATCAGACAAGGGTATCTGTCTAAACGTTCCTCAAACTTGAGAGGTGACTGGAAAAGAAGATTCTTTATCCTTGATAGCCGTGGGATGCTAT
upper sequence: GLYMA05G38550.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv17s0000g00310.t01 (Vitis vinifera), 3'ss of exon 11
---gtattttagaatttgacgtttccttctttctgagatt-----tatgtattacttcattttaaaacttttcaattctgagttgagtcctgtccattgccgtttcttcatc---gcttgcaaaattttagGTTCAAATCATTCGACAAGGATATCTTTCTAAACGATCCTCCAATTTGAGAGGTGACTGGAAAAGAAGGTATTTTGTTGTTGACAGTCGAGGAATGTTGT
| || ||| || ||||||| | ||| | | | ||| |||| ||| | | ||||| || || | | ||| | | | | | | ||| | | ||||||||| ||||||||||||||||||||| ||||| ||||| |||||||| ||||||||||| ||||||| |||||| |||| || ||||| |||||||
gtaatggttgagatgaccacctttcctttctagtgactctaggaatctaaatttcttcctttctagcatccctcattcttttttaagcagtattaatttaaatatatgtagctaagacagcactagtgcagGTTCAAACCATTCGACAAGGATATCTTTCAAAACGTTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTTCTTTGTTCTTGATAGCCGAGGCATGTTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattctgagttgagtcctgtccattgccgtttcttcatcgcttgcaaaattttagGTTCAAATCATTCGACAAGGATATCTTTCTAAACGATCCTCCAATTTGAGAGGTGACTGGAAAAGAAGGTATTTTGTTGTTGACAGTCGAGGAATGTTGT
aaaatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttagaatttgacgtttccttctttctgagatttatgtattacttcattttaaaacttttcaattctgagttgagtcctgtccattgccgtttcttcatcgcttgcaaaattttagGTTCAAATCATTCGACAAGGATATCTTTCTAAACGATCCTCCAATTTGAGAGGTGACTGGAAAAGAAGGTATTTTGTTGTTGACAGTCGAGGAATGTTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG