Sequence
atgc intronic sequence ATGC exonic sequencegtattctgagtttctaatctaaatttaatattttcagtttttcaccttattttttggcaatgaaacaagtcacattgatccaactcattgatgaaatttatgcagGTAAAATTTGACCAGTTTGTTGAGCAAGGGCGTGTTCTTCATAATTATGCTTCAATATTGGAGTTACTTTTACGTCTTCGGCAATGTTGTGATCATCCAT
Basic information
species | Glycine max |
transcript | GLYMA12G30540.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G30540.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os02g32570.1 (Oryza sativa), 3'ss of exon 13
gtattctgagtttctaatctaaatttaatattttcagtttttcaccttattttttggcaatgaaacaagtcacattgatccaactcattgatgaaatttatgcagGTAAAATTTGACCAGTTTGTTGAGCAAGGGCGTGTTCTTCATAATTATGCTTCAATATTGGAGTTACTTTTACGTCTTCGGCAATGTTGTGATCATCCAT
|||| | || || |||| | | | || ||| | || |||| |||||| | || ||| | ||| |||| |||||||| || || || || ||||| | || | || |||||||||||||| |||||||| ||||| || |||||||| |||||||| || ||||
-------------gtaatgcatcttcaaccaaagaagttctactcgtttggattt--ctgagagacaa-----attgat---agtc-ttgttctgctttg-atagGTGAAATTTGATCAATTCGTGGAACAAGGAAGGGTCTTGCACAATTATGCTTCAATTTTGGAGTTGCTTTTGCGCCTTCGGCAGTGTTGTGACCACCCAT
upper sequence: GLYMA12G30540.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G057504_T01 (Zea mays), 3'ss of exon 2
gtattctgagtttctaatctaaatttaatat-tttcagtttttcaccttattttttggcaatgaaacaagtcacattgatccaactcattgatgaaatttatgcagGTAAAATTTGACCAGTTTGTTGAGCAAGGGCGTGTTCTTCATAATTATGCTTCAATATTGGAGTTACTTTTACGTCTTCGGCAATGTTGTGATCATCCAT
|||| ||| | | | | |||| ||| || ||||||| | | |||| ||||| | ||||||||||||| || |||||||||||||| | ||||| || || ||||||||||| |||||||||||||| || || ||||||| |||||||||||||
------------------------gtaatgcgcttctactgataagcgtattcttt--cagggaaacaaatta-attgccttg---tgttgat--------tatagGTAAAATTTGATCAATTTGTTGAGCAAGGAAGGGTTCTGCACAACTATGCTTCAATTTTGGAGTTACTTTTGCGCCTAAGGCAATGCTGTGATCATCCAT
upper sequence: GLYMA12G30540.1 (Glycine max), 3'ss of exon 14
lower sequence: AT5G22750.1 (Arabidopsis thaliana), 3'ss of exon 13
gtattctgagtttctaatctaaatttaatattttcagtttttcaccttattttttggcaatgaaacaagtcacattgatccaactcattgatgaaatttatgcagGTAAAATTTGACCAGTTTGTTGAGCAAGGGCGTGTTCTTCATAATTATGCTTCAATATTGGAGTTACTTTTACGTCTTCGGCAATGTTGTGATCATCCAT
| | | | || || || || | ||| | | | | | | | | ||| | ||| | | || | ||||| |||||||| || |||||||| ||||| ||||||||||| |||||||| || |||| | ||||| |||||||| |||||||||||||| ||||
-------------------gtattgttttccttaggattatttactcgaactttagttattaagatgccttatactga----agatgctgacggatctttttcagGTCAAATTTGATCAATTTGTTGAACAAGGCAAAGTTCTTCATAACTATGCTTCGATCCTGGAACTGCTTTTGCGTCTTCGACAATGTTGTGATCACCCAT
upper sequence: GLYMA12G30540.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv06s0061g01190.t01 (Vitis vinifera), 3'ss of exon 13
gtattctgagtttctaatctaaatttaatattttcagtttttcaccttattttt-tggcaatgaaacaagtcacattgatccaactcattgatgaaatttatgcagGTAAAATTTGACCAGTTTGTTGAGCAAGGGCGTGTTCTTCATAATTATGCTTCAATATTGGAGTTACTTTTACGTCTTCGGCAATGTTGTGATCATCCAT
| | || | || ||| || | || || |||||| || | | | | || | | | ||||| || || | ||||| || ||||| || |||||||||||||| || |||||||||||||||||||| || |||||||| |||||| ||||||| |||||||||||||||||||
-----------gtattccctgacttaaatgattgta----ttgactgcatttttctgattttagtatgacaccttttctttaatttgattga--aacattcttcagGTGAAGTTTGATCAATTTGTTGAGCAAGGACGGGTTCTTCATAATTATGCTTCTATTTTGGAGTTGCTTTTATGTCTTCGCCAATGTTGTGATCATCCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttggcaatgaaacaagtcacattgatccaactcattgatgaaatttatgcagGTAAAATTTGACCAGTTTGTTGAGCAAGGGCGTGTTCTTCATAATTATGCTTCAATATTGGAGTTACTTTTACGTCTTCGGCAATGTTGTGATCATCCAT
cattgat putative branch site (score: 4)
attgatgaaatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattctgagtttctaatctaaatttaatattttcagtttttcaccttattttttggcaatgaaacaagtcacattgatccaactcattgatgaaatttatgcagGTAAAATTTGACCAGTTTGTTGAGCAAGGGCGTGTTCTTCATAATTATGCTTCAATATTGGAGTTACTTTTACGTCTTCGGCAATGTTGTGATCATCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG