Sequence
atgc intronic sequence ATGC exonic sequence...attgcagatctgtgtctggtgctggcaccacataatggacatggctgagaaggatgacactgaggggcgatgccctgcatgtcgttctccttatgataagGAAAAGATTGTTGGGACGGCTGCAAACT
Basic information
species | Glycine max |
transcript | GLYMA12G07790.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G07790.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g01190.3 (Oryza sativa), 3'ss of exon 2
----------------------------------------------------------------------attgcagatctgtgtctggtgctggcaccacataatggacatggctgagaaggatgacactgaggggcgatgccctgcatgtcgttctccttatgataagGAAAAGATTGTTGGGACGGCTGCAAACT
| ||||||| ||||||||||||||||||||||| || || ||||||||||| || ||||||||||| || ||||| ||||| || ||| ||||| || || | ||
gtttcttcccttccctccccaccactctactctccacaccccccttccattcacctcccttttgcatctcactgcagATTTGTGTCTGGTGCTGGCACCACATCATTGATATGGCTGAGAAAGAGGACACTGAGGGCCGCTGCCCCGCATGCCGCACTCGCTATGACAAAGATAGGA---------------------
upper sequence: GLYMA12G07790.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g01190.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------------------------------------attgcagatctgtgtctggtgctggcaccacataatggacatggctgagaaggatgacactgaggggcgatgccctgcatgtcgttctccttatgataagGAAAAGATTGTTGGGACGGCTGCAAACT
| ||||||| ||||||||||||||||||||||| || || ||||||||||| || ||||||||||| || ||||| ||||| || ||| ||||| || || | ||
gtttcttcccttcccttccctcccctccccaccactctactctccacacccccttccattcacctcccttttgcatctccactgcagATTTGTGTCTGGTGCTGGCACCACATCATTGATATGGCTGAGAAAGAGGACACTGAGGGCCGCTGCCCCGCATGCCGCACTCGCTATGACAAAGATAGGA---------------------
upper sequence: GLYMA12G07790.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G146267_T02 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------------------------------attgcagatctgtgtctggtgctggcaccacataatggacatggctgagaaggatgacactgaggggcgatgccctgcatgtcgttctccttatgataagGAAAAGATTGTTGGGACGGCTGCAAACT
||||||| ||||| ||||||||||||||||| || ||||||||||||||||| || || | ||| || ||||||||||| || | ||||| ||||| | ||
gtatgtctactgattctcctatcctattgtaccaatcagattgcagcccaccttgtctgcactttgtttcatcatataacaagaactgtcacttaactctgcagATTTGTGTTTGGTGCTGGCACCACATCATAGACATGGCTGAGAAGGAGGAAACAGTGGGCCGCTGCCCTGCATGCCGCACATGCTATGACAAGGACAGGA---------------------
upper sequence: GLYMA12G07790.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G400238_T02 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------------------------attgcagatctgtgtctggtgctggcaccacataatggacatggctgagaaggatgacactgaggggcgatgccctgcatgtcgttctccttatgataagGAAAAGATTGTTGGGACGGCTGCAAACT
||||||| ||||| ||||||||||||||||| || ||||||||||||||||| || || | ||| || ||||||||||| || | ||||| ||||| | ||
gtatgtctactgatcttcttcctatcctatcaatcatattgcagcctgccttgcatgcactttgtgccatcatctaacaataactgccataactctgcagATTTGTGTTTGGTGCTGGCACCACATCATAGACATGGCTGAGAAGGAGGAAACAGTGGGCCGCTGCCCTGCATGCCGCACATGCTATGACAAGGACAGGA---------------------
upper sequence: GLYMA12G07790.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G848541_T02 (Zea mays), 3'ss of exon 7
--------------------------------------------------------------attgcagatctgtgtctggtgctggcaccacataatggacatggctgagaaggatgacactgaggggcgatgccctgcatgtcgttctccttatgataagGAAAAGATTGTTGGGACGGCTGCAAACT-------
| ||||| ||||| | || |||||||||||| || ||||||||||||||||| || || |||| || |||||||| || | | | |||||| ||||| | ||| || || ||| || | |
gatcaattagattgcagcctgccttgcatgcactgtgcgccatcatcaaataactgctacttaactcagatttgtgtttcgtactggcaccacatcatagACATGGCTGAGAAGGAGGAAACAAAGGGCCGCTGCCCTGCCTGCCACACACGTTATGACAAGGATATGATCGTCAAGATGGCCGCCACTTGTGACAG
upper sequence: GLYMA12G07790.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g03580.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------------------------------------------------------attgcagatctgtgtctggtgctggcaccacataatggacatggctgagaaggatgacactgaggggcgatgccctgcatgtcgttctccttatgataagGAAAAGATTGTTGGGACGGCTGCAAACT
|| ||||| ||||| ||||||||||| ||||||||| ||||||||||||||||||| || ||||| || ||||||||||| ||| |||||| | || |||||||
tattgaaccatttgtatctgatttcatcccttattcatcaactggaaagccttaaaattgtttccactccatttgtaattctgcttgtgtgtctttacagATATGTGTTTGGTGCTGGCATCACATAATGAACATGGCTGAGAAGGATGAAACAGAGGGTCGGTGCCCTGCATGCCGTGTCCCTTATAACAAAGAAAAGA--------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagaaggatgacactgaggggcgatgccctgcatgtcgttctccttatgataagGAAAAGATTGTTGGGACGGCTGCAAACT
tcgttctcctt CT-rich tract
ttatgataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgcagatctgtgtctggtgctggcaccacataatggacatggctgagaaggatgacactgaggggcgatgccctgcatgtcgttctccttatgataagGAAAAGATTGTTGGGACGGCTGCAAACT
- - - -atctgtg
- - - - - - - -ctggtgc
- - - - - - - - - - - - -caccaca
- - - - - - - - - - - - - - - - - - - -catggct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgagggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctgca