Sequence
atgc intronic sequence ATGC exonic sequence...tcctttttgaattacaaattgtccgctttattttgttctttcaattttgctagttatagatatacagcgcaattgaatgatcaatttttgttcaattcagATCCCACCAAATTCAGCTGGCCTCATTGAGTATAGAGCACATCCTTTCTGGCGACAAAAATATTGTCCATCGCATGAGGGTGATGGTACTCCTCGTTGTT
Basic information
species | Glycine max |
transcript | GLYMA16G25750.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 6
-tcctttttgaattacaaattgtccgc-tttattttgtt-ctttcaatt-ttgctagttatagatataca-gcgcaattgaatgatcaatttttgttcaattcagATCCCACCAAATTCAGCTGGCCTCATTGAGTATAGAGCACATCCTTTCTGGCGACAAAAATATTGTCCATCGCATGAGGGTGATGGTACTCCTCGTTGTT
|| | | || |||| | | | || || | | | || || || | | || | |||| || | | || || |||||||| || ||||| |||||| ||||| ||||||||||||||||||||| ||||||||| |||||||| ||||||| || |||||||| | || |
aataattgacatgtgaaagttgttaacatgtgttaagtaacagccgacaatttctttttgtttttttaaatgcgccatcttacagttccttctt-----attcagATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCT
upper sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------------------tcctttttgaattacaaattgtccgctttattttg---------ttctttcaattttgctagttatagatataca-gcgcaattgaatgatcaatttttgttcaattcagATCCCACCAAATTCAGCTGGCCTCATTGAGTATAGAGCACATCCTTTCTGGCGACAAAAATATTGTCCATCGCATGAGGGTGATGGTACTCCTCGTTGTT
| || | | || || | || | ||| ||| | | || | || | | || || || | | ||| ||| | | ||||||| || ||||| |||||| ||||| ||||| ||||||||||||||| ||||||||| ||||| || ||||| ||||||||||| | || |
gtaaggatcactttatttaccctgaccgatctgtttatgctataagttttttctgttgaacattttacttgcctgtttgtgctaataaaatctatctccaatatcttggagaatgtgctttctctacatttttcatgattgacatgtttactcttgctaatatctgattacttctt--ttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT
upper sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 6
tcctttttgaattacaaattgtccgctttattttgttctttc--aattttgctagttatagatatacagcgcaat-tgaatgatcaatttttgttcaattcagATCCCACCAAATTCAGCTGGCCTCATTGAGTATAGAGCACATCCTTTCTGGCGACAAAAATATTGTCCATCGCATGAGGGTGATGGTACTCCTCGTTGTT
| ||| ||| || | | | | || | | || |||| | || ||| ||| || ||| || | | || | |||| || ||||| ||||||| || ||||||||||| |||||||| || ||| ||||| |||||||| || |||||| ||||||| |||||||| ||||
--gtgagtgatagccaacttctgttgatctctatattttacccaaaatttgttcccaggttgtactaagcttaatgtgtatgtataaatgtaactcc-tctagATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTT
upper sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0023g01040.t01 (Vitis vinifera), 3'ss of exon 10
tcctttttgaattacaaattgtccgctttattttgttctttcaattttgctagttatagat-atacagcgcaattgaatgatcaatttttgttcaattcagATCCCACCAAATTCAGCTGGCCTCATTGAGTATAGAGCACATCCTTTCTGGCGACAAAAATATTGTCCATCGCATGAGGGTGATGGTACTCCTCGTTGTT
| |||| | || | ||| | | ||| || | | | | || | | | | || |||| | ||| | | ||| || | ||||| ||| ||||| ||||||| | |||||||||||||||||||||||| ||| | || ||||| || |||||| |||||| |||||||| ||||
-cattttgaagaaactagatgtgcaatgtatatttgtttcttttgtatgtttttcacaaatgatactgtagcattaatgtaattctttcccttttgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTT
upper sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 7
tcctttttgaatta-caaattgtccgctttattttgttctttcaattttgctagttatagat-atacagcgcaattgaatgatcaatttttgttcaattcagATCCCACCAAATTCAGCTGGCCTCATTGAGTATAGAGCACATCCTTTCTGGCGACAAAAATATTGTCCATCGCATGAGGGTGATGGTACTCCTCGTTGTT
|||||||| | | | ||| | | ||| || | | | | || | | | | || |||| | || | || ||| || | ||||| ||| ||||| ||||||| || |||||||||||||||||||| |||||| ||||| || ||||| || || ||| |||||| |||||||| ||||
--tattttgaataaactagatgtgcaatgtatatttgtttcttttgtatgtttttcacaaatgatactgtagcatcaatgtatttctttcctttttgtacagATTCCAACAAATGCAGCTGGACTTATTGAGTATAGAGCACATCCGTTCTGGATGCAAAAGTACTGTCCCTCACACGAGCATGATGGAACTCCTCGGTGTT
upper sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ07250 (Selaginella moellendorffii), 3'ss of exon 2
tcctttttgaattacaaattgtccgctttattttgttctttcaattttgctagttatagatatacagcgcaattgaatgatcaatttttgttcaattcagATCCCACCAAATTCAGCTGGCCTCATTGAGTATAGAGCACATCCTTTCTGGCGACAAAAATATTGTCCATCGCATGAGGGTGATGGTACTCCTCGTTGTT
| | | ||| || | || | || || || | || ||| ||||||| ||||| ||||| ||||||| || ||||| | ||||||||||||||| ||||||| ||||| || | |||||| || || ||||| ||||
-------------------------------------------gtatgttttgttg-agctttata-tgcggatgg--tatttacttccagtca-ttcagATTCCACCGAATTCCTCTGGCCTGATAGAGTACCGCGCACATCCTTTCTGGGGACAAAAGTATTGCCCCTTGCATGAAAAGGACTCCACCCCTCGATGTT
upper sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ07867 (Selaginella moellendorffii), 3'ss of exon 2
tcctttttgaattacaaattgtccgctttattttgttctttcaattttgctagttatagatatacagcgcaattgaatgatcaatttttgttcaattcagATCCCACCAAATTCAGCTGGCCTCATTGAGTATAGAGCACATCCTTTCTGGCGACAAAAATATTGTCCATCGCATGAGGGTGATGGTACTCCTCGTTGTT
| | | ||| || | || | || || || | || ||| ||||||| ||||| ||||| ||||||| || ||||| | ||||||||||||||| ||||||| ||||| || | ||| || || || ||||| ||||
-------------------------------------------gtatgttttgttg-agctttata-tgcggatgg--tatttacttccagtca-ttcagATTCCACCGAATTCCTCTGGCCTGATAGAGTACCGCGCACATCCTTTCTGGGGACAAAAGTATTGCCCCTTGCACGAAAAGGACTCCACCCCTCGATGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgctagttatagatatacagcgcaattgaatgatcaatttttgttcaattcagATCCCACCAAATTCAGCTGGCCTCATTGAGTATAGAGCACATCCTTTCTGGCGACAAAAATATTGTCCATCGCATGAGGGTGATGGTACTCCTCGTTGTT
tttttgttc CT-rich tract
aatttttgttcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcctttttgaattacaaattgtccgctttattttgttctttcaattttgctagttatagatatacagcgcaattgaatgatcaatttttgttcaattcagATCCCACCAAATTCAGCTGGCCTCATTGAGTATAGAGCACATCCTTTCTGGCGACAAAAATATTGTCCATCGCATGAGGGTGATGGTACTCCTCGTTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatga