Sequence
atgc intronic sequence ATGC exonic sequence...ccttttttgaattagaattgtccactttattttgttctttcaactttttctagttatagatataaagtacaattgaatgattgatttttgttcattgcagATTCCACCAAATTCAGCTGGTCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTT
Basic information
species | Glycine max |
transcript | GLYMA12G19010.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G19010.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 6
--ccttttttgaattagaattgtccac-tttattttgtt-ctttcaactttttctagttatagatataaa-gtacaattgaatgattgatttttgttcattgcagATTCCACCAAATTCAGCTGGTCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTT
|| | | | |||| || | | || || | | || ||||| || | | |||| | | || | || || || |||| |||||| ||||| ||| || ||||| ||||||||||||||||||||| |||||||||| |||||||| |||||| || |||||||| | || |
aataattgacatgtgaaagttgttaacatgtgttaagtaacagccgacaatttctttttgtttttttaaatgcgccatcttacagttccttcttattca-----gATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCT
upper sequence: GLYMA12G19010.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 6
------------------------------------------------------------------------ccttttttg--aattagaattgtccactttattttg---------ttctttcaactttttctagttatagatataaagtacaattg--aatgattgatttttgttcattgcagATTCCACCAAATTCAGCTGGTCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTT
| ||| || ||| | | | || | ||| ||| | | || || |||| | | || || || ||| ||| ||| ||||| | || || |||||||| ||||| ||| || ||||| ||||| ||||||||||||||| |||||||||| ||||| || ||||| ||||||||||| | || |
gtaaggatcactttatttaccctgaccgatctgtttatgctataagttttttctgttgaacattttacttgcctgtttgtgctaataaaatctatctccaatatcttggagaatgtgctttctctacatttttca-tgattgacatgtt-tactcttgctaatatctgattact--tcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT
upper sequence: GLYMA12G19010.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 6
----ccttttttgaattagaattgtccactttattttgttctttcaactttttctagttatagatataaagtacaattgaatgattgatttttgttcattgcagATTCCACCAAATTCAGCTGGTCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTT
| || | ||| | || |||||| | || | ||| || ||| | | || ||| | | | | || | ||||||| ||||| |||||||||| ||||||||||| |||||||| || ||| | ||||| |||||||| || |||||||||||||| |||||||| ||||
gtgagtgatagccaacttctgttgatctctatattttacccaaaatttgttcccaggttgtac---taagcttaatgtgtatgtataaatgtaactcctc-tagATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTT
upper sequence: GLYMA12G19010.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g01040.t01 (Vitis vinifera), 3'ss of exon 10
ccttttttgaattagaattgtccactttat-tttgttctttcaactttttctagttatagat-ataaagtacaattgaatgattgatttttgttcattgcagATTCCACCAAATTCAGCTGGTCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTT
| |||| | | ||| || | ||| |||||| || | || | | | | || ||| ||| ||| | | | ||| || | ||||||||| ||||| ||||||| | |||||||||||||||||||||||| | ||| | || ||||| || ||||||| |||||| |||||||| ||||
cattttgaagaaactagatgtgcaatgtatatttgtttcttttgtatgtttt--tcacaaatgatactgtagcattaatgtaattctttcccttttgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTT
upper sequence: GLYMA12G19010.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 7
ccttttttgaattag--aattgtccactttat-tttgttctttcaactttttctagttatagat-ataaagtacaattgaatgattgatttttgttcattgcagATTCCACCAAATTCAGCTGGTCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTT
| |||||||| | | ||| || | ||| |||||| || | || | | | | || ||| ||| || | ||| ||| || | ||||||||| ||||| ||||||| || |||||||||||||||||||| |||||| | ||||| || ||||| || || |||| |||||| |||||||| ||||
--tattttgaataaactagatgtgcaatgtatatttgtttcttttgtatgtttt--tcacaaatgatactgtagcatcaatgtatttctttcctttttgtacagATTCCAACAAATGCAGCTGGACTTATTGAGTATAGAGCACATCCGTTCTGGATGCAAAAGTACTGTCCCTCACACGAGCATGATGGAACTCCTCGGTGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctagttatagatataaagtacaattgaatgattgatttttgttcattgcagATTCCACCAAATTCAGCTGGTCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTT
gattgat putative branch site (score: 4)
tttttgttc CT-rich tract
ttatagatataaagta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccttttttgaattagaattgtccactttattttgttctttcaactttttctagttatagatataaagtacaattgaatgattgatttttgttcattgcagATTCCACCAAATTCAGCTGGTCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - tgtccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatga