Sequence
atgc intronic sequence ATGC exonic sequence...tactattccaaaaccttaagctgttgggtgaaaacacatgactgacttctctaacaataattgtgattttaagttagatttgatcataactgtgatgcagGTATGAGGATGCTTTTAATAGGTTTATTGATGAAATCAACTCGGTTGCTGCATATGATTGGTGGGAGGGATCAGTGCACAGTATACTTTCTGTTGTTGCA
Basic information
species | Glycine max |
transcript | GLYMA01G41140.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G41140.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os04g10380.1 (Oryza sativa), 3'ss of exon 15
tactattccaaaaccttaagctgttgggtgaaaacacatgactgacttctctaacaataattgtgattttaagttagatttgatcataactgtgatgc-agGTATGAGGATGCTTTTAATAGGTTTATTGATGAAATCAACTCGGTTGCTGCATATGATTGGTGGGAGGGATCAGTGCACAGTATACTTTCTGTTGTTGCA
||||| || | | | | | || | | | | | | | || | | || || | || | | | | | ||| || ||||| ||||||||||| | ||||| ||||| ||||| | ||| |||||||| || |||||||| ||||| | || ||||||||||| || |||||
aactatgtcatatatattt-ccgaagaatgttcatgtctccatcagtattttgtttgtattccttgccataggtgatatcttgttactttttttttgccagATATGAAGATGCTTTTAACCGTTTTATCGATGAGATCAATTTGGTGGCTGCATACGAGTGGTGGGAAGGATCTATACATAGTATACTTTCAGTACTTGCA
upper sequence: GLYMA01G41140.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G015291_T01 (Zea mays), 3'ss of exon 7
-----tactattccaaaaccttaagctgttgggtgaaaacacatgactgacttctctaacaataattgtgattttaagttagatttgatcataactgtgatgcagGTATGAGGATGCTTTTAATAGGTTTATTGATGAAATCAACTCGGTTGCTGCATATGATTGGTGGGAGGGATCAGTGCACAGTATACTTTCTGTTGTTGCA
| ||| | | | | || || ||| || |||||| | | | | || || | || | || | | | | ||| ||||| |||||||| || | ||||||||||| ||||| | ||| ||||||||||| |||||||| ||||| | || ||||||||||||||| ||||
atctattctaacttgaggaaatgatttattttcccaag-taca-gaatgacttgtgagaaatacagaaacatcagaactaagctctgtttttttccttt---cagTTATGAAGATGCTTTCAACCGTTTTATTGATGAGATCAATTTGGTGGCTGCATATGAGTGGTGGGAAGGATCTATACATAGTATACTTTCTGTTCTTGCG
upper sequence: GLYMA01G41140.1 (Glycine max), 3'ss of exon 15
lower sequence: AT5G47020.1 (Arabidopsis thaliana), 3'ss of exon 16
tactattccaaaaccttaagctgttgg-gtgaaaacaca---tgactgacttctctaacaataattgtgattttaagttagatttgatcataactgtgatgcagGTATGAGGATGCTTTTAATAGGTTTATTGATGAAATCAACTCGGTTGCTGCATATGATTGGTGGGAGGGATCAGTGCACAGTATACTTTCTGTTGTTGCA
| | | | ||| | | |||| | | || || |||| | | ||| ||| | | ||| | || ||| ||| ||||||| || ||||||||||| || |||||| ||||||| ||||| || ||||||||||||||||| || || |||||||| || ||||| ||| |||||
cgttttcttatactctttgcttatcaatgtgacatcgtcctttggctcactt-tattccaaggcatgtccactca---tagttctggacatttctgattcgcagGTACGAAGATGCTTTTAACAGCTTTATTAATGAAATAAACTCTACCGCAGCATATGATTGGTGGGAAGGGTCTGTGCACAGCATTCTTTCAGTTCTTGCA
upper sequence: GLYMA01G41140.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv02s0012g00460.t01 (Vitis vinifera), 3'ss of exon 15
tactattccaaaaccttaagctgttgggtgaaaacacatgactgacttctctaacaataattgtgattttaagttagatttgatcata--------actgtgat--gcagGTATGAGGATGCTTTTAATAGGTTTATTGATGAAATCAACTCGGTTGCTGCATATGATTGGTGGGAGGGATCAGTGCACAGTATACTTTCTGTTGTTGCA
| || | || | |||| | |||| || | | | | || | ||||| || | ||| | ||| | | |||| ||||||||| ||||||||||| || || |||||||| || || || ||||||||||||||||||||||| || ||||| ||||| |||||||| || |||||
-------ttagaagcctattgtattgga--agaacatattagcatcaggttgtgccatc-tcatgattcaaaaaaatgttttctaatattctgactattttgatctacagGTATGAAGATGCTTTTAACAGATTCATTGATGAGATTAATTCAGTTGCTGCATATGATTGGTGGGAAGGGTCAGTACACAGCATACTTTCAGTGCTTGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttctctaacaataattgtgattttaagttagatttgatcataactgtgatgcagGTATGAGGATGCTTTTAATAGGTTTATTGATGAAATCAACTCGGTTGCTGCATATGATTGGTGGGAGGGATCAGTGCACAGTATACTTTCTGTTGTTGCA
tcataac putative branch site (score: 2)
taacaataattgtgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tactattccaaaaccttaagctgttgggtgaaaacacatgactgacttctctaacaataattgtgattttaagttagatttgatcataactgtgatgcagGTATGAGGATGCTTTTAATAGGTTTATTGATGAAATCAACTCGGTTGCTGCATATGATTGGTGGGAGGGATCAGTGCACAGTATACTTTCTGTTGTTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - caaaacc
- - - - - - - - - - -tgttggg
- - - - - - - - - - - - - - - - aacacat