Sequence
atgc intronic sequence ATGC exonic sequencegtatctatgtcattgctagtttgacttactagagttattgacatatccccttgtgctgttcttggatcttgtacaatttaatataaaatcctttactggtgatggtactcatctacttttaataacttaaacagTTTGGCAATTGCAAAAGAAGGTGAGCTTACTATTGGCACCATTGATGATATACAAAAACTTCATATTCGCTCTATTCCACTGGGGGAGCATGCACGACGT
Basic information
species | Glycine max |
transcript | GLYMA05G30530.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G430027_T01 (Zea mays), 3'ss of exon 4
gtatctatgtcattgctagtttgacttactagagttattgacatatccccttgtgctgttcttggatcttgtacaatttaatataaaatcctttactggtgatggtactcatctacttttaataacttaaacagTTTGGCAATTGCAAAAGAAGGTGAGCTTACTATTGGCACCATTGATGATATACAAAAACTTCATATTCGCTCTATTCCACTGGGGGAGCATGCACGACGT
| | | | || | || || | ||||| ||| | || | | | | | | || | | | || | | | |||| || | |||| | |||||||| ||||| ||||||||| | ||||| || ||||||||||| || || |||||||| ||| | || || || || || ||||| ||
-------------------------tcatttgtgtcactggtctagtca-ttgtggagttacag----ttagaaagtattac-cactgtcttaaggttcctctagttcacccttcttttttccaatgt---cagTCTTGCAATTGCTAAAGAGGGTGAGCTTTCAATTGGAACTATTGATGATATCCAGAAGCTTCATATCCGCACAATCCCCCTTAATGAACAAGCACGCCGC
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 16
lower sequence: AT4G05420.2 (Arabidopsis thaliana), 3'ss of exon 15
gtatctatgtcattgctagtttgacttactagagttattgacatatccccttgtgctgtt-cttggatcttgtacaatttaatataaaatcctttactggtgatggtactcatctacttttaataactta--aacagTTTGGCAATTGCAAAAGAAGGTGAGCTTACTATTGGCACCATTGATGATATACAAAAACTTCATATTCGCTCTATTCCACTGGGGGAGCATGCACGACGT
|||| | | | | | | | | | | || ||| || || || | | |||| || | | ||| || | | | | || |||| | |||||| |||||||| | |||||||| ||||| ||||| |||||||||||||| || || ||||| || || ||||||| || || |||||||| || ||
-----------------------gtacactaaacatcctctctttttcttgtcggtttttgctttgaatttcta-attcctatatgaagc---taagtggctctgaaatctgattctctgttctatcttatgagcagTTTAGCAATTGCCAGGGAAGGTGAACTTACGATTGGAACCATTGATGATATTCAGAAGCTTCACATACGTACTATTCCTCTTGGAGAGCATGCTCGTCGA
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 16
gtatctatgtcattgctagtttgacttactagagttattgacatatccccttgtgctgttcttggatcttgtacaatttaatataaaatcctttactggtgatggtactcatctacttttaataacttaaacagTTTGGCAATTGCAAAAGAAGGTGAGCTTACTATTGGCACCATTGATGATATACAAAAACTTCATATTCGCTCTATTCCACTGGGGGAGCATGCACGACGT
|| ||| | || ||| | | || ||| | | || ||| | | | | | ||||||| | ||| | | ||| ||| | |||||||| ||||||||||| ||||| || || |||||||||||||| || || ||||| || |||||||| ||||| ||||||||||| || ||
------------ccatgagcttggtacaagtaagaggctgagaa----------gatgaaattgtaaatgatattattgggttaagagac--taactggtggcttttctccccctttctta----------cagCCTTGCAATTGCCAAAGAAGGTGATCTTACAATCGGTACCATTGATGATATCCAGAAGCTTCACATCCGCTCTATCCCACTTGGGGAGCATGCTCGCCGC
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 16
lower sequence: PP1S203_55V6.1 (Physcomitrella patens), 3'ss of exon 16
gtatctatgtcattgctagtttgacttactagagttattgacatatccccttgtgctgttcttggatcttgt--acaatttaatataaaatcctttactggtgatggtactcatctacttttaataacttaaacagTTTGGCAATTGCAAAAGAAGGTGAGCTTACTATTGGCACCATTGATGATATACAAAAACTTCATATTCGCTCTATTCCACTGGGGGAGCATGCACGACGT
|| || |||| | ||||| | ||| | || | || | || | ||| | | || | | | || ||| ||||||| |||| | || || | ||| ||||| ||||| || || ||||||||||||||||| ||||| |||||||||||| | |||| || || || | | | |||
--------------------------------cagcataga-atattactttgtgtcatactttaaatttatgaactagttga-atacattaaagtaaggaccttcatgactgactgatttcgataacttc--cagTCTTGCCATCGGAAAGGAAGGGGAGCTCACAATCGGCACCATTGATGATATTCAAAAGCTTCATATTCGCACAGTTCCTCTTGGCGAACGCCCTTGCCGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatataaaatcctttactggtgatggtactcatctacttttaataacttaaacagTTTGGCAATTGCAAAAGAAGGTGAGCTTACTATTGGCACCATTGATGATATACAAAAACTTCATATTCGCTCTATTCCACTGGGGGAGCATGCACGACGT
taataac putative branch site (score: 1)
atctacttttaataac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctatgtcattgctagtttgacttactagagttattgacatatccccttgtgctgttcttggatcttgtacaatttaatataaaatcctttactggtgatggtactcatctacttttaataacttaaacagTTTGGCAATTGCAAAAGAAGGTGAGCTTACTATTGGCACCATTGATGATATACAAAAACTTCATATTCGCTCTATTCCACTGGGGGAGCATGCACGACGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA