Sequence
atgc intronic sequence ATGC exonic sequence...ggaagtagtaattgaactattgcagattgctctttaattaattgtttctccttgacatatgaatggggtcactttcttacttttacatttttacttgtagGTGAAACTTGAAGTGATGGGGAAAAAGGCAAAGAATGCAACCTATATATCTGGAAATGAAGCAGGGAAGATCTCAAAAGAAATTCAGAAAGTGGAGAAGC
Basic information
species | Glycine max |
transcript | GLYMA20G34970.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34970.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g56540.1 (Oryza sativa), 3'ss of exon 1
ggaagtagtaattgaactattgcag-attgctctttaattaattgtttctccttgacatatgaatggggtcactttcttacttttacat-ttttacttgtagGTGAAACTTGAAGTGATGGGGAAAAAGGCAAAGAATGCAACCTATATATCTGGAAATGAAGCAGGGAAGATCTCAAAAGAAATTCAGAAAGTGGAGAAGC
| | | | ||| | | | | | ||| | | || || || || || | | | | | |||| || ||| || || ||||| |||||||| || || |||||||||||||| ||||||||||||||||| |||||||| |||| |||| || |||||||| |||
--atatgatggacagaagattttaatagttttaactgcgtaactttggaaattttctatggtgttgaagtttctcagtccttactccttactttatgtgcagGCGAGGCTAGAAGTAATGGGGAAGAAAGCCAAGAATGCAACCTACATATCTGGAAATGAAGCCGGGAAGATATCAAGAGAAGTTGCAAAAGTGGAAAAGA
upper sequence: GLYMA20G34970.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G062084_T01 (Zea mays), 3'ss of exon 1
-----ggaagtagtaattgaactattgcag-attgctctttaattaattgtttctccttgacatatgaatggggtcactttcttacttttacatttttacttgtagGTGAAACTTGAAGTGATGGGGAAAAAGGCAAAGAATGCAACCTATATATCTGGAAATGAAGCAGGGAAGATCTCAAAAGAAATTCAGAAAGTGGAGAAGC
| | || || ||| | | || | || || || |||| | | ||| || | | | || || | | || ||| || ||| ||||| |||||||| || || |||||||||||||||||||||||||||||| | || | ||| |||| |||| || ||||| || ||||
attatgaatgttgtcattcatttgttctgtcaatgtaaatttatggattgatgtaaatcagtgtatcgttgaagcc------tcacagttctgtatctatggacagGCGAGACTAGAAGTAATGGGGAAGAAAGCTAAGAATGCAACCTATATATCTGGAAATGAACCTGGAAGGATATCAAGAGAAGTTTCTAAAGTTGAAAAGC
upper sequence: GLYMA20G34970.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G062084_T02 (Zea mays), 3'ss of exon 1
-----ggaagtagtaattgaactattgcag-attgctctttaattaattgtttctccttgacatatgaatggggtcactttcttacttttacatttttacttgtagGTGAAACTTGAAGTGATGGGGAAAAAGGCAAAGAATGCAACCTATATATCTGGAAATGAAGCAGGGAAGATCTCAAAAGAAATTCAGAAAGTGGAGAAGC
| | || || ||| | | || | || || || |||| | | ||| || | | | || || | | || ||| || ||| ||||| |||||||| || || |||||||||||||||||||||||||||||| | || | ||| |||| |||| || |||
attatgaatgttgtcattcatttgttctgtcaatgtaaatttatggattgatgtaaatcagtgtatcgttgaagcc------tcacagttctgtatctatggacagGCGAGACTAGAAGTAATGGGGAAGAAAGCTAAGAATGCAACCTATATATCTGGAAATGAACCTGGAAGGATATCAAGAGAAGTTTCTAAA----------
upper sequence: GLYMA20G34970.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G150984_T02 (Zea mays), 3'ss of exon 1
ggaagtagtaattgaactattgcagattgctctttaattaattgtttctccttgacatatgaatggggtcacttt-----cttacttttacatttttacttgtagGTGAAACTTGAAGTGATGGGGAAAAAGGCAAAGAATGCAACCTATATATCTGGAAATGAAGCAGGGAAGATCTCAAAAGAAATTCAGAAAGTGGAGAAGC
|| | ||| | | || | || | | ||| | || |||| || | | || | || || | || | | || ||| ||||| ||||| ||||||||||| || ||||| |||| |||||||||||||||||||| |||| ||| |||| |||| | || ||||| || |
---tgttttcattcatttcttcttggccactgtcgatgtaaat-ttatgaattgatgta-aagcagtgtatcgttgaagcctcgcagttctgtatctatgcacagGCAAAACTGGAAGTAATGGGGAAAAAAGCGAAGAACGCAAGTTATATATCTGGAAATGAAGCTGGGAGGATATCAAGAGAAGTGTTTAAGGTGGAAAAAC
upper sequence: GLYMA20G34970.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0049g01350.t01 (Vitis vinifera), 3'ss of exon 1
ggaagtagtaattgaactattgcagattgctctttaattaattgtttctccttgacatatgaatggggtcactttcttacttttacattttt--------acttgtagGTGAAACTTGAAGTGATGGGGAAAAAGGCAAAGAATGCAACCTATATATCTGGAAATGAAGCAGGGAAGATCTCAAAAGAAATTCAGAAAGTGGAGAAGC
| |||| | || || | ||| |||| ||| | | || | | ||||| | | ||| | || |||| | | ||| |||||| ||| ||||| ||||| || ||||| ||||||||||||| ||||||||||| |||||| || ||||| || ||||| || || |||||||||||||
--------tctttgatacaatggaggtcttatttttattatggcttttgcttgaaccttcaattggggcaatgtacttgccttactatttcttatttcggatttgcagGTGAGACTAGAAGTAATGGGAAAGAAGGCCAAGAATGCAACCTTTATATCTGGAACTGAAGCCGGAAAGATATCTAAAGAGATCCAAAAAGTGGAGAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctccttgacatatgaatggggtcactttcttacttttacatttttacttgtagGTGAAACTTGAAGTGATGGGGAAAAAGGCAAAGAATGCAACCTATATATCTGGAAATGAAGCAGGGAAGATCTCAAAAGAAATTCAGAAAGTGGAGAAGC
ttcttac putative branch site (score: 2)
ctttcttacttttaca CT-rich tract
tttcttacttttacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggaagtagtaattgaactattgcagattgctctttaattaattgtttctccttgacatatgaatggggtcactttcttacttttacatttttacttgtagGTGAAACTTGAAGTGATGGGGAAAAAGGCAAAGAATGCAACCTATATATCTGGAAATGAAGCAGGGAAGATCTCAAAAGAAATTCAGAAAGTGGAGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - -tattgca
- - - - - - - - - - - - - - - - - - - - - - - -ctccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatgg