Sequence
atgc intronic sequence ATGC exonic sequencegtatgccttttcattatgaaaccttacctgatgacaagtatatctagtttatgtacaaagctgcaattaccttcaagttatagatttgctgatactggatgtgttgttacagATGCAACATGATTATATTTTGGGAAATTACCCTATTGGAAGGGATGATGCTGCTCAGCTCTCTGCATTACAAATTTTGGCTGAGATTGGATTTCTCAACA
Basic information
species | Glycine max |
transcript | GLYMA09G32740.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 6
gtatgccttttcattatgaaaccttacctgatgac--aagtatatctagtttatgtacaaagctgcaattaccttcaagttatagatttgctga-tactggatgtgttgttacagATGCAACATGATTATATTTTGGGAAATTACCCTATTGGAAGGGATGATGCTGCTCAGCTCTCTGCATTACAAATTTTGGCTGAGATTGGATTTCTCAACA
| || ||| | | ||| |||| | | || | | | | | | | || | || |||||| || | | || | | ||| | ||||||||||||||||| ||||| || || | || |||||||||||||| ||||| ||||| | ||||| |||| || ||||| ||| | |||
------------gtactgg--cctgggcagctgattgaagtgctgccaattcttacgtta--cagaagtaatattgtttccttggaagtgctgactaatataattgctat-gcagTTACAACATGATTATATTTTAGGAAACTATCCAGTAGGTAGGGATGATGCTGCACAGCTATCTGCTCTGCAAATATTGGTCGAAATTGGCTTTGTTGACA
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 7
gtatgccttttcattatgaaaccttacctgatgacaagtatatctagtttatgtacaaagctgcaattaccttcaagttatagattt-gctgatactggatgtgttgttacagATGCAACATGATTATATTTTGGGAAATTACCCTATTGGAAGGGATGATGCTGCTCAGCTCTCTGCATTACAAATTTTGGCTGAGATTGGATTTCTCAACA
| ||| || || | ||||| ||| | | ||| || | | | | || ||| | | | | | | ||| ||||||||||||| ||||||||||| || ||| |||| |||||||||||| | || |||||||| | ||||| |||| |||||||||||| || |||
---------------------------gtactga--aggattgccagtttgtgtgtta---ttcaagtaatcttggttcaaaaatagagctaacaagtaacattgttctgcagTTGCAACATGATTACATTTTGGGAAACTATCCTGTTGGCAGGGATGATGCTTCACAACTCTCTGCTCTGCAAATCTTGGTTGAGATTGGATTCATCGACA
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 6
gtatgccttttcattatgaaaccttacctgatgacaagtatatctagtttatgtac-aaagctgc--aattaccttcaagttatagatttg--ctgatactggatgtgttgttacagATGCAACATGATTATATTTTGGGAAATTACCCTATTGGAAGGGATGATGCTGCTCAGCTCTCTGCATTACAAATTTTGGCTGAGATTGGATTTCTCAACA
||| || | ||| | || || | ||| | | ||||| ||| | | | | || || | || ||| | | || | | | || | ||| ||||||||||||| ||||||||||| || ||| | || |||||||||||| | || |||||||| | || || |||| |||||||||||| | | |
gtactggttgatagtattcatagctagctaactg-aaggactgccagtttgtgtgttattgttactcaagtaatattgt-ttccagaatagatctaacaaatatcatttttctgcagTTGCAACATGATTACATTTTGGGAAACTATCCTGTCGGCAGGGATGATGCTTCACAACTCTCTGCTCTTCAGATCTTGGTTGAGATTGGATTCATTGATA
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------gtatgccttttcattatgaaaccttacctgatgacaagtatatctagtttatgtacaaagctgcaattaccttcaagttatagatttgctgatactggatgt-gttgttacagATGCAACATGATTATATTTTGGGAAATTACCCTATTGGAAGGGATGATGCTGCTCAGCTCTCTGCATTACAAATTTTGGCTGAGATTGGATTTCTCAACA
| || | || || || | |||| | | ||| | | | || | || || || |||| | ||| | | | ||||| ||| |||||||||| ||||| ||||| ||||| ||| ||||||| ||||||||||| || || |||||||| || |||||| |||||||||||| |
gtatgtaatcttattttaaagtaatttgtgagcaactctgattaatatttgaatatgtacaactttgactaactatgggaattttgaacaggcagtatctgatttaagctttgatctaacttgtttttattgtttcagTTGCAACATGACTATATATTGGGCAATTATCCTGTTGGAAGAGATGATGCTGCACAACTATCTGCATTGCAGATTTTGATTGAGATTGGATTCATTGGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagctgcaattaccttcaagttatagatttgctgatactggatgtgttgttacagATGCAACATGATTATATTTTGGGAAATTACCCTATTGGAAGGGATGATGCTGCTCAGCTCTCTGCATTACAAATTTTGGCTGAGATTGGATTTCTCAACA
tgctgat putative branch site (score: 3)
ttatagattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgccttttcattatgaaaccttacctgatgacaagtatatctagtttatgtacaaagctgcaattaccttcaagttatagatttgctgatactggatgtgttgttacagATGCAACATGATTATATTTTGGGAAATTACCCTATTGGAAGGGATGATGCTGCTCAGCTCTCTGCATTACAAATTTTGGCTGAGATTGGATTTCTCAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC