Sequence
atgc intronic sequence ATGC exonic sequencegtagggctatgcttctacatcttttagtttttctctagcatcaatactctccctgcatctacactttaataccatcttttaaattttatattttgacctttttctcagTATATAAGAAGCATTATCCACCAGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTCCATAAGAAGCTGAATAATGCAGG
Basic information
species | Glycine max |
transcript | GLYMA13G01160.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5
gtagggctatgcttctacatcttttagtttttctctagcatcaatactctccctgcatctacactttaataccatcttttaaattttatattttgacctttttctcagTATATAAGAAGCATTATCCACCAGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTCCATAAGAAGCTGAATAATGCAGG
|| | ||| |||| | || | | || | | ||| ||| |||| | || | ||| | ||| | ||| ||||||||||| || ||||| || |||| ||||| || ||||| || || |||||||| |||||||| || |||||||||| ||||| || || ||
-----------------------gtaagtcctctgaagcaaccatgatatgatacgatt--cttcatgatatt-tctattaactgtttgaatttca---tttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 5
gtagggctatgcttctacatcttttagtttttctctagcatcaatactctccctgcatctacactttaataccatcttttaaattttatattttgacctttttctcagTATATAAGAAGCATTATCCACCAGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTCCATAAGAAGCTGAATAATGCAGG
|| || | | || || ||| || ||||| | | || | | || | || | ||| | | | | ||| || |||||||| |||||||| || ||| ||||| || ||||| ||||| || ||||| |||||||||||||||||||||| |||||| || | ||
--------------------------gtaagtcccaaaaatgtatctgtgtactgtattcccactt-gacat-atatctaaactatttcaatttcatttatct---agTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G010471_T01 (Zea mays), 3'ss of exon 1
gtagggctatgcttctacatcttttagtttttctctagcatcaatactctccctgcatctacactttaataccatcttttaaattttatattttgacctttttctcagTATATAAGAAGCATTATCCACCAGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTCCATAAGAAGCTGAATAATGCAGG
|| || | | || || ||| || ||||| | | || | | || | || | ||| | | | | ||| || |||||||| |||||||| || ||| ||||| || ||||| ||||| || ||||| |||||||||||||||||||||| |||||| || | ||
--------------------------gtaagtcccaaaaatgtatttgtgtgctgtattctcactt-gacat-atatctaaactatttcaatttcatttatct---agTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 5
gtagggctatgcttctacatcttttagtttttctctagcatcaatactctccctgcatctacactttaataccatcttttaaattttatattttgacctttttctcagTATATAAGAAGCATTATCCACCAGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTCCATAAGAAGCTGAATAATGCAGG
|| || | | || | | | || || | | || | || || | | || | || | || | ||| | ||| || |||||||| |||||||| | | | ||||| || ||||| ||||| || ||||| |||||||| ||||||||||||| |||||| || | ||
--------------------------gtaagtcccaa-----aaaattgtttttgtatttcta--ttgacac-atatctaaactattccagattca---tttacctagTGTACAAGAAGCACTATCCACCTACGCTAAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGAAAGGATGGCTCATTCCATAAGAGGCTGAACAAATCTGG
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 5
lower sequence: AC202073.4_FGT001 (Zea mays), 3'ss of exon 4
gtagggctatgcttctacatcttttagtttttctctagcatcaatactctccctgcatctacactttaataccatcttttaaattttatattttgac---ctttttctcagTATATAAGAAGCATTATCCACCAGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTCCATAAGAAGCTGAA-TAATGCAGG
| ||| | ||| | || | | || | || ||| |||| || | ||| || || || ||| ||| ||||||||||||||||| || ||| | | ||||| || |||||||| || ||||| || |||||||| |||||||| |||| | || | | | |
------------------------gtatgtttatttagtgt-gatgtcattgttaaat--aatctaacatataggctttaaacatgaatacgttaactaactcttttgtagTGTATAAGAAGCATTATCCTCCTGCACTAAAGGATGAGGTATGGAGATTAGAAAAGATTGGAAAGGATGGTTCATTCCACAAGAGATTAAACTCAAGTGG-
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
gtagggctatgcttctacatcttttagtttttctctagcatcaatactctccctgcatctacactttaataccatcttttaaattt-tatattttgacctttttctcagTATATAAGAAGCATTATCCACCAGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTCCATAAGAAGCTGAATAATGCAGG
|||| | || | | |||| ||| ||| | | ||||| |||| | ||||||| || | | || || | |||| || ||||||||||||||||| || ||| |||||| |||||||||||||| ||||| |||||||||||| |||||||||| ||||| | | || |||
------gtatggtcttaaaagctccccttttcttct--------cactgtac---catctggtgtttact----tcttttagtttgatgcacatttcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 5
gtagggctatgcttctacatcttttagtttttctctagcatcaatactctccctgcatctacactttaataccatcttttaaattttatattttgacctttttctcagTATATAAGAAGCATTATCCACCAGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTCCATAAGAAGCTGAATAATGCAGG
|||| | | | | || | ||| | | | || | | || | | | | ||| | | || | | | | || ||| || | ||| || ||||||||||||||||| || |||| |||||| |||||||| || |||||||| || || |||||| | || ||||||| ||| | ||||||
------gtatgtgttttc-ttttcttgttctctttttgcct---tgtgcttgccacttgttttcttctaaatcaacatgt---tgttggattg----gttatgtgtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCTAACCGCTGCAGG
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 4
gtagggctatgct--tctacatcttttagtttttctctagcatcaatactctccctgcatctacactttaataccatctt-ttaaattttatattttgacctttttctcagTATATAAGAAGCATTATCCACCAGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTCCATAAGAAGCTGAATAATGCAGG
||||| | ||| || ||||||| || || | | | | ||| ||| || | || ||| || || ||| | | |||| ||| | ||| |||||||| || |||||||| ||||| |||||||| |||||||||||||||||||| ||||||||||| |||||||| |||| ||| |||||| |
gtaggttcaggctcatccttgtcttttatttattgaattattttattgttctttt----tcttatctgtgatgacatgttattgaatctgctgtttttccctgggt---agTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcatctacactttaataccatcttttaaattttatattttgacctttttctcagTATATAAGAAGCATTATCCACCAGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTCCATAAGAAGCTGAATAATGCAGG
ttttgac putative branch site (score: 3)
ttttgacctttttctc CT-rich tract
tacactttaataccat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagggctatgcttctacatcttttagtttttctctagcatcaatactctccctgcatctacactttaataccatcttttaaattttatattttgacctttttctcagTATATAAGAAGCATTATCCACCAGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTCCATAAGAAGCTGAATAATGCAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA