Sequence
atgc intronic sequence ATGC exonic sequence...ttgtgtgatggtgtgtataatgttttaaatattgaatgatgaaatataactccttggcattgagtttgacaacactttctcttgtgacatcttgacacagGTTAGTGCCTCATATGAGCAGGCTTTGGTGGATGCACGCAAGCTAATTGAGCGGGAAATGGAAAGATTTAAGATATGTGAGAAGGAAACTAAGACCAAAG
Basic information
species | Glycine max |
transcript | GLYMA16G04690.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G04690.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 2
-ttgtgtgatggtgtgtataatgttttaaatattgaatgatgaaatataactccttggcattgagtttgacaacactttctcttgtgacatcttgacacagGTTAGTGCCTCATATGAGCAGGCTTTGGTGGATGCACGCAAGCTAATTGAGCGGGAAATGGAAAGATTTAAGATATGTGAGAAGGAAACTAAGACCAAAG-----
|||| |||| | | | | ||| |||| | || || ||| || || |||| || | ||| | | | | | |||||| ||||||||||||| |||||||||||| | ||||||| || |||| ||||| || || |||||| |||||||| | ||||||||||||||||| || || |
tttgtatgata-tattt-tgccgttgcaaatgacttttttgttaacattacttactgtt-ctgggtttaac--ccatttataatat-atgtgttgacataggttagTGCCTCTTATGAGCAGGCTCTTATGGATGCCCGAAAGCAGATTGAACGCGAGATGGAACGATTTAAGGTTTGTGAGAAGGAAACTAAAACGAAGGCCTTT
upper sequence: GLYMA16G04690.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g44900.1 (Oryza sativa), 3'ss of exon 2
ttgtgtgatggtgtgtataatgttttaaatattgaatgatgaaatataactccttggcattgagtttgacaacactttctcttgtgacatcttgacacagGTTAGTGCCTCATATGAGCAGGCTTTGGTGGATGCACGCAAGCTAATTGAGCGGGAAATGGAAAGATTTAAGATATGTGAGAAGGAAACTAAGACCAAAG---------------------
| ||| |||| | || || ||| || || |||| || | ||| | | | | | |||||| ||||||||||||| |||||||||||| | ||||||| || |||| ||||| || || |||||| |||||||| | ||||||||||||||||| || || |
-----------------tgccgttgcaaatgacttttttgttaacattacttactgtt-ctgggtttaac--ccatttataatat-atgtgttgacataggttagtgcctcttatgagcagGCTCTTATGGATGCCCGAAAGCAGATTGAACGCGAGATGGAACGATTTAAGGTTTGTGAGAAGGAAACTAAAACGAAGGCCTTTTCCAAGGAAGGGTTAG
upper sequence: GLYMA16G04690.1 (Glycine max), 3'ss of exon 2
lower sequence: AC197122.3_FGT003 (Zea mays), 3'ss of exon 3
ttgtgtgatggtgtgtataatgttttaaatattgaatgatgaaatataa--ctccttggcattgagtt-tgacaacactttctcttgtgacatcttgacacagGTTAGTGCCTCATATGAGCAGGCTTTGGTGGATGCACGCAAGCTAATTGAGCGGGAAATGGAAAGATTTAAGATATGTGAGAAGGAAACTAAGACCAAAG
| || || | | ||| | ||| | || | ||| || | | | | | | | | ||| || | || | || | || |||||| ||||||||||||| |||||||||||| || ||||||| || |||| ||||| || || |||||| ||||||| |||||||||||||||| || || || |
cttcatg-tgatata-atactcgtttgcgaaatgca-gataaatttttagtttacataccctactgttctggttttaattgattgtgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGATGGATGCTCGAAAGCAGATTGAACGAGAGATGGAACGATTTAAAGTATGTGAGAAGGAAACAAAAACTAAGG
upper sequence: GLYMA16G04690.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 2
---ttgtgtgatggtgtgtataatgttttaaatattgaatgatgaaatataactccttggcattgagtttgacaacactttctcttgtgacatct--tgacacagGTTAGTGCCTCATATGAGCAGGCTTTGGTGGATGCACGCAAGCTAATTGAGCGGGAAATGGAAAGATTTAAGATATGTGAGAAGGAAACTAAGACCAAAG
| | | | |||| || |||| |||| | |||| ||||| ||||||| ||| |||||| ||| | || ||| || | ||||| ||||||||||||| |||||||||||| || ||||||| || ||||| || ||||| |||||||||||||||||||||||||| || ||||||||||| ||||
ggataattttagcttgtggattctgttgataata----actatgacatata-ctccttgattctgaagttgacagttatttgttttttgatatatgttgacatagGTTAGTGCCTCTTATGAGCAGGCTCTGCTGGATGCTCGGAAGCTTATCGAGCGTGAAATGGAAAGATTTAAGATATGTGAAAAAGAAACTAAGACAAAAG
upper sequence: GLYMA16G04690.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S101_120V6.1 (Physcomitrella patens), 3'ss of exon 3
ttgtgtgatggtgtgtataatgttttaaatattgaatgatgaaatataactccttggcattgagtttgacaacactttctcttgtgacatcttgacacagGTTAGTGCCTCATATGAGCAGGCTTTGGTGGATGCACGCAAGCTAATTGAGCGGGAAATGGAAAGATTTAAGATATGTGAGAAGGAAACTAAGACCAAAG---------------------
| | ||| || | | | || || || || | | | || | | | | |||| | | | ||| | | | | | | ||||||| | || || || |||| || ||| | ||||||||||||||||| |||||||||||||||| ||||| ||||
--------------gaaggatggattgattctctcataattgaa---aaagtttagatactggaatag-tggggtgtaatgttgttaatagtattcctgtgtt--ttctttgtg-gtgtagGCTTTACTTGAGGCTCGGAAGCAGATAGAGAGAGAAATGGAAAGATTTAAAGTATGTGAGAAGGAAACCAAGACAAAAGCATTTTCCAAAGAAGGCCTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataactccttggcattgagtttgacaacactttctcttgtgacatcttgacacagGTTAGTGCCTCATATGAGCAGGCTTTGGTGGATGCACGCAAGCTAATTGAGCGGGAAATGGAAAGATTTAAGATATGTGAGAAGGAAACTAAGACCAAAG
tcttgac putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtgtgatggtgtgtataatgttttaaatattgaatgatgaaatataactccttggcattgagtttgacaacactttctcttgtgacatcttgacacagGTTAGTGCCTCATATGAGCAGGCTTTGGTGGATGCACGCAAGCTAATTGAGCGGGAAATGGAAAGATTTAAGATATGTGAGAAGGAAACTAAGACCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA