Sequence
atgc intronic sequence ATGC exonic sequencegtcagatgtcagttttttaggctgtttaattctctgctgatatttcatgccttgaccagacagtccctttgaggtattacagttgttttctcatatggcctttgttgggggttgaatttggtgaatatttggcttgcagTTCTATGTTGATACAGTGAAGCAAATGGCACTTCGCCAGCTGATTGCAGGGTCACCTTTGCGCACATTATGCCTTCTAATTGCTGGGCAACCTGCTGAAG
Basic information
species | Glycine max |
transcript | GLYMA11G03580.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G03580.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g01490.1 (Oryza sativa), 3'ss of exon 4
gtcagatgtcagttttttaggctgtttaattctctgctgatatttcatgccttgaccagacagtccctttgaggtattac-agttgttttctcatatggcctttgttgggggttgaatttggtgaatatttggcttgcagTTCTATGTTGATACAGTGAAGCAAATGGCACTTCGCCAGCTGATTGCAGGGTCACCTTTGCGCACATTATGCCTTCTAATTGCTGGGCAACCTGCTGAAG
|||| || | || || ||| || | ||| || | ||| |||| | | || | || | | | ||| || | | | | | | ||||||| || || ||||| |||||| ||||||| | |||| | | | |||||||||||||| ||||| |||||||| |||||||| |||||||| || |
-----------gtttgttcgacttaatagccttctcttgtt------tgcatt---tgaatagtttgcttgattttcaatgaggttttcttttccttaattttttttatttatcttttctt-tccccaccggtggtgcagTTTTACGTCGATACTGTGAAGAAAATGGCCCACTGCCATTTTCTATCTGGGTCACCTTTGCGAACATTGTGCCTTCTCATTGCTGGACAACCTGCAGATG
upper sequence: GLYMA11G03580.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G47480.1 (Arabidopsis thaliana), 3'ss of exon 4
gtcagatgtcagttttttaggctgtttaattctctgctgatatttcatgccttgaccagacagtccctttgaggtattacagttgttttc-tcatatggcctttgttgggggttgaatttggtgaatatttggcttgcagTTCTATGTTGATACAGTGAAGCAAATGGCACTTCGCCAGCTGATTGCAGGGTCACCTTTGCGCACATTATGCCTTCTAATTGCTGGGCAACCTGCTGAAG
| | || |||| | || || | | | | | | |||| | | ||||||| | ||||||||||||||| || || ||||| |||||||| |||||||||||||| | ||||||||||| || ||||| ||||| || |||| || ||||| |||||||
---------------------------------------------------------gttcctttcccttgat-tgctatagaactaaacgttccactgtagtgcttggttgactgacttggtgatgtcctaacttgcagTTCTATGTAGACACTGTGAAACAAATGGCCCTTCGCCAGCTGATACCCGGGTCACCTTTACGGACATTGTGCCTACTCGTTGCGGGACAACCAGCTGAAG
upper sequence: GLYMA11G03580.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G47490.1 (Arabidopsis thaliana), 3'ss of exon 4
gtcagatgtcagttttttaggctgtttaattctctgctgatatttcatgccttgaccagacagtccctttgaggtattacagttgttttc-tcatatggcctttgttgggggttgaatttggtgaatatttggcttg---cagTTCTATGTTGATACAGTGAAGCAAATGGCACTTCGCCAGCTGATTGCAGGGTCACCTTTGCGCACATTATGCCTTCTAATTGCTGGGCAACCTGCTGAAG
| || || | | || || | | | | | | |||| | | ||||| || | | ||| |||||||||||||| || ||||| |||||||| |||||||||||| | | ||||||||||| || ||| | ||||| || |||| |||||||| |||||||
----------------------------------------------------------gtttgtttctcttgattgctatagaactaaacattgcactgtagtgcttggttgactgacttggtcgatgtcttaattgatgcagTTCTATGTTGACACTGTGAAACAAATGGCCCTTCGCCAGCTGGTACCCGGGTCACCTTTACGAACACTGTGCCTGCTGGTTGCAGGGCAACCAGCTGAAG
upper sequence: GLYMA11G03580.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0229g00030.t01 (Vitis vinifera), 3'ss of exon 4
gtcagatgtcagttttttaggctgtttaattctctgctgatatttcatgccttgaccagacagtccctttgaggtattacagttgttttctcatatggcctttgttgggggttgaatttggtgaatatttggctt----gcagTTCTATGTTGATACAGTGAAGCAAATGGCACTTCGCCAGCTGATTGCAGGGTCACCTTTGCGCACATTATGCCTTCTAATTGCTGGGCAACCTGCTGAAG
||| || || || | | | | |||| || | || | || || |||| ||||| | |||||| ||||||||||| || |||||||||||| |||||||||| | |||| ||||||||||| ||| |||| || ||||||||||| ||||| ||||| |
-------------------------------------------------gtttgtcctgat-----tcttaaactcatttatcatttttttccaacaatgactggcagtaatttgcttgggtgtggttttggaatcaatgcagTTTTATGTTGATACTGTTAAGCAAATGGCAATTCGCCAGCTAGTACCAGGATCACCTTTGCGGACACTATGTCTGCTAATTGCTGGACAACCGGCTGATG
upper sequence: GLYMA11G03580.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 5
-gtcagatgtcagttttttaggctgtttaattctctgctgatatttcatgccttgaccaga-cagtccctttgaggtattacagttgttttctcatatggc---ctttgttgggggttgaatttggtgaatatttggctt-------------gcagTTCTATGTTGATACAGTGAAGCAAATGGCACTTCGCCAGCTGATTGCAGGGTCACCTTTGCGCACATTATGCCTTCTAATTGCTGGGCAACCTGCTGAAG
|| || || | || |||| | || | | | ||| | | | || ||| | | | | || || || ||| | | | || || || | | | | | | || |||||| |||| |||||| ||||||||||||||||||| ||| | ||||||| ||||||||||| || || ||||| ||||||| ||||| || || || |
gttctcatacaagcatatttaattgtt---ctttccattcctttaccatatttgaattggctcaatcctgatctagcagaggaattcattccttggatgtcaaacctgatttcaatttttatgctgacactctcttgtttcctttaatttcatgcagTTTTATGGTGATACCGTGAAGCAAATGGCACTTCAGCAGTTAGTTGCAGGATCACCTTTGCGGACGTTGTGCCTGTTAATTGCAGGGCAGCCAGCAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttctcatatggcctttgttgggggttgaatttggtgaatatttggcttgcagTTCTATGTTGATACAGTGAAGCAAATGGCACTTCGCCAGCTGATTGCAGGGTCACCTTTGCGCACATTATGCCTTCTAATTGCTGGGCAACCTGCTGAAG
tgaatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagatgtcagttttttaggctgtttaattctctgctgatatttcatgccttgaccagacagtccctttgaggtattacagttgttttctcatatggcctttgttgggggttgaatttggtgaatatttggcttgcagTTCTATGTTGATACAGTGAAGCAAATGGCACTTCGCCAGCTGATTGCAGGGTCACCTTTGCGCACATTATGCCTTCTAATTGCTGGGCAACCTGCTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG