Sequence
atgc intronic sequence ATGC exonic sequence...ttatactttatatttcgtgggcatgataccttgtacctgtactgataatttatatcttttgtactaatagaagtgtcttggtgcttgttgtctatggcagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
Basic information
species | Glycine max |
transcript | GLYMA13G17610.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os07g37750.1 (Oryza sativa), 3'ss of exon 17
ttatactttatatttcgtgggcatgataccttgtacctgtactgataatttatatcttttgtactaatagaagtgtcttggtgcttgttgtctatggcagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
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--------------gtatgtgtataaagtcttaatgct--acttttatttgacatgtcaaccactg------gtctcaaatggtatattatgacttgcagGTACTGTGCTGATAACCCTGGACTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCTTATGCTGTTATAATGTTGAATACTGACGCCCACAACCCAATG
upper sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 18
ttatactttatatttcgtgggcatgataccttgtacctgtactgataatttatatcttttgtactaa----tagaagtgtcttggtgcttgt-tgtctatg-gcagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
| | | | ||||| | || | | || ||||| | | | | | || | ||| ||| |||| |||||||| || ||||||| ||||| |||||||||||||| ||||||||||| |||||||||||||| ||||| ||||||||||| || || ||||||
--------------------gtaggtttatatgtacttatagaaaacacaaatttctttaagattttgcccccgtcaccctcagatactgatatgtttatttgcagGTACTGTGCTGATAATCCTGAGCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCTTATGCTGTTATAATGTTGAATACTGATGCACACAATCCAATG
upper sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 20
lower sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 19
------------------------------------------------------ttatactttatattt---cgtgggcatgataccttgtacctgtactgataatttatatcttttg------tactaatagaagtgtcttggtgc-ttgttgtctatggcagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
||| ||| || || |||| | | | | | | || | || |||| ||| || ||| | | | || | | ||||| || | ||||| || ||||||||||| || ||||| || |||||||||||||| || |||||||| ||||| ||||| ||||||||||| ||||| ||||| || |||
gtaagggcgccatgtattattctctgagatcattatatgaatctagtacaaatattaagcttggtagttatttgtggattaggtgaatggaaaatctatatttggttcttatcattttcccagttaataactaacatattatgttccactgttgccttgagtagATATTGCGCAGACAATCCGGGTCTTTTCAAGAATGCAGATACAGCCTACGTTCTAGCCTATGCAGTTATCATGTTAAATACAGATGCGCATAATCCTATG
upper sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 20
ttatactttatatttcgtgggcatgataccttgtacctgtactgataat--ttatatcttttgtactaataga-agtgtcttggtgcttgttgt-------ctatggcagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
| | | | |||||| || ||| | | || | |||| || | ||| ||| | || ||| |||| || |||||| ||||||||||||||||| | ||||| |||||||||||||| ||||||||||| || ||||| ||||| ||||| ||||||||||| ||||| || |||
----------ttgagtgaaaaaaggttaccttctaggtgtcatcaagatcatgtcccctttcttattgctagttggtgatctagtcctttttgtgttttgtctctggcagTTACTGTGCAGACAATCCAGATCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCATATGCAGTTATAATGTTGAATACTGATGCACATAATCCCATG
upper sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 20
lower sequence: PP1S122_29V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------------------------ttatactttatatttcgtgggcatgataccttgtacctgtactg----ataatttatatcttttgtactaatagaagtgtcttggtgctt---gttgtctatggcagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
|| || | | | | | || | | || | | | || | | || | | ||| | || || || ||| | || ||| |||||| ||| ||| | |||||| ||||||||||| ||||||||||| || || ||||| ||||||||| | || || ||||||||||| || |
gttgaacttttaatcatgttttctcatatcgtcattgcagttggcggttaatttaggtggccgagaaattatcagaacccttaaacgctatttcaagtaccttcgagataagggcagatatcagcaatgtgtcgtgacgtaacacctgccggctatttcttctgactatgtactttggataagtgattacagGTACTGTCGAGATAATGGTAACCTTTTCAAAAATGCAGACACAGCTTATGTGCTGGCGTATGCAGTTATTATGCTCAACACAGATGCTCATAATCCTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatttatatcttttgtactaatagaagtgtcttggtgcttgttgtctatggcagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatactttatatttcgtgggcatgataccttgtacctgtactgataatttatatcttttgtactaatagaagtgtcttggtgcttgttgtctatggcagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - gcatgat
- - - - - - - - - - - - - - ccttgta
- - - - - - - - - - - - - - - - - -cctgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgct