Sequence
atgc intronic sequence ATGC exonic sequencegtaatggcttttctgtacttgcaagtgtctcagggtgttttataaggtgtcaaatcttggttgattgtcatgtcataatgtctacttacactttatatttcgtgggcatgataccttgcatggttgtacctgtactgataatttatatcttttgtactaatagcagtgtctttgtgcatgttgtctatgacagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
Basic information
species | Glycine max |
transcript | GLYMA17G04890.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G04890.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os07g37750.1 (Oryza sativa), 3'ss of exon 17
gtaatggcttttctgtacttgcaagtgtctcagggtgttttataaggtgtcaaatcttggttgattgtcatgtcataatgtctacttacactttatatttcgtgggcatgataccttgcatggttgtacctgtactgataatttatatcttttgtactaat-agcagtgtctttgtgcatgttgtctatgacagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
| || | | || || || ||| ||| | | || | || || | || || | | ||| |||||||| || || ||||| ||||| |||||||||||||| ||||||||||| |||||||||||||| ||||| |||||||| || || |||||||||
-------------------------------------------------------------------------------------------------------------------gtatgtgtataaagtcttaatgctacttt-tatttgacatgtcaaccactggtctcaaatggtatattatgacttgcagGTACTGTGCTGATAACCCTGGACTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCTTATGCTGTTATAATGTTGAATACTGACGCCCACAACCCAATG
upper sequence: GLYMA17G04890.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 18
gtaatggcttttctgtacttgcaagtgtctcagggtgttttataaggtgtcaaatcttggttgattgtcatgtcataatgtctacttacactttatatttcgtgggcatgataccttgcatggttgtacctg-tactgataatttatatcttttgtactaatagcagtgtctttgtgcatgttgtctatgacagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
| | | || || || || || | ||||| | | | | | || || | | | ||| |||||||| || ||||||| ||||| |||||||||||||| ||||||||||| |||||||||||||| ||||| ||||||||||| || || ||||||
-----------------------------------------------------------------------------------------------------------gtaggtttatatgtacttatagaaaacacaaatttctttaagattttgcccccgtcaccctcagatactg-atatgtttatttgcagGTACTGTGCTGATAATCCTGAGCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCTTATGCTGTTATAATGTTGAATACTGATGCACACAATCCAATG
upper sequence: GLYMA17G04890.1 (Glycine max), 3'ss of exon 20
lower sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 19
gtaatggcttttctgtacttgcaagtgtctcagggtgttttataaggtgtcaaatcttggttgattgtcatgtcataatgtctacttacactttatatttcgtgggcatgatacct-tgcatggttgtacctgtactgataatttatatcttttgtactaatagcagtgtctttgtgcatgttgtctatgacagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
|||| ||| |||| | | | ||| || || ||| | |||| | | | | | | | | | || || | ||| ||| | | || | ||||| | | | | || ||| || || || ||| ||||| || ||||| || ||||||||||| || ||||| || |||||||||||||| || |||||||| ||||| ||||| ||||||||||| ||||| ||||| || |||
gtaagggcgcca-tgtatt----attctctgagatcattatatga--------atctagtacaaatattaag-cttggtagttatttg-----tggattaggtgaatggaaaatctatatttggttcttatcattttcccagttaataactaacatatta-------tgttcca----ctgttgccttgagtagATATTGCGCAGACAATCCGGGTCTTTTCAAGAATGCAGATACAGCCTACGTTCTAGCCTATGCAGTTATCATGTTAAATACAGATGCGCATAATCCTATG
upper sequence: GLYMA17G04890.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 20
gtaatggcttttctgtacttgcaagtgtctcagggtgttttataaggtgtcaaatcttggttgattgtcatgtcataatgtctacttacactttatatttcgtgggcatgataccttgcatggttgtacctgtactgataatttatatcttttgtactaat-agcagtgt----ctttgtgcatgttgtctatgacagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
|| ||| | | | ||| | || | |||| | | ||| | | | | |||| || | |||||| || ||| ||||||||||||||||| | ||||| |||||||||||||| ||||||||||| || ||||| ||||| ||||| ||||||||||| ||||| || |||
-------------------------------------------------------------------------------------------------ttgagtgaaaaaaggttaccttctaggtgtcatcaagatcatgtcccctttcttat-tgctagttggtgatctagtcctttttgtgttttgtctctggcagTTACTGTGCAGACAATCCAGATCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCATATGCAGTTATAATGTTGAATACTGATGCACATAATCCCATG
upper sequence: GLYMA17G04890.1 (Glycine max), 3'ss of exon 20
lower sequence: PP1S122_29V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaatggcttttctgtacttgcaagtgtctcagggtgttttataaggtgtcaaat--cttggttgattgtcatgtcataatgtctacttacactttatatttcgtgggcatgataccttgcatggttgtacc--tgtactgataatttatatcttttgtactaatagcagtgtctttgtgcat---gttgtctatgacagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
| | || | | || | ||||| || | || || | | || | || | | | || | | |||| || ||| | || || | | | | | | ||| | | | | | || | ||| | || || ||| | | | || |||| |||||| ||| ||| | |||||| ||||||||||| ||||||||||| || || ||||| ||||||||| | || || ||||||||||| || |
---gttgaacttttaatcatgt---tttctcatatcgtcattgcagttggcggttaatttaggtggccgagaaattatcagaacc-cttaaacgctatttcaagtaccttcgagataagggcagatatcagcaatgtgtcgtgacgtaacacctgccg-gctatttcttctgactatgtactttggataagtgattacagGTACTGTCGAGATAATGGTAACCTTTTCAAAAATGCAGACACAGCTTATGTGCTGGCGTATGCAGTTATTATGCTCAACACAGATGCTCATAATCCTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatttatatcttttgtactaatagcagtgtctttgtgcatgttgtctatgacagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
tactaat putative branch site (score: 1)
tatatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatggcttttctgtacttgcaagtgtctcagggtgttttataaggtgtcaaatcttggttgattgtcatgtcataatgtctacttacactttatatttcgtgggcatgataccttgcatggttgtacctgtactgataatttatatcttttgtactaatagcagtgtctttgtgcatgttgtctatgacagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT