Sequence
atgc intronic sequence ATGC exonic sequence...aataattgtttcaaaaatgttattgatcaatttagtcattctcctttatttatcattttgaatggatgatgactttagtttttgttttgtttctccttcaGGTTGCTGTTGCACATACAATAGGACATGTAGCGGCAACAGTTAGTATGTCAAAAGTTGCGGTATCGTTTACACATATTATCAAGAGTGGTGAACCTGCT
Basic information
species | Glycine max |
transcript | GLYMA18G12080.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G12080.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g08840.2 (Oryza sativa), 3'ss of exon 2
aataattgtttcaaaaatgttattgatcaatttagtcattctcctttatttatcattttgaatggatgatgactttagtttttgttttgtttctccttcaGGTTGCTGTTGCACATACAATAGGACATGTAGCGGCAACAGTTAGTATGTCAAAAGTTGCGGTATCGTTTACACATATTATCAAGAGTGGTGAACCTGCT-
|| | || | || | ||||| | | | || | | | ||| |||| || |||| | | | || || | |||||||||| || |||||||| || ||||| || || ||||| |||||||||||||| || || || || ||||| |||||||| |||| || |||||
-----gtgagtggaatctttttcttggcaatt--atttgtatatttgctgtgcctgcttgggcaagc-atga--ttgattttggctattttccttttgaagGTTGCTGTGGCTCATACAATTGGGCATGTTGCTGCGACAGTGAGTATGTCAAAAGTAGCAGTGTCATTCACACACATTATCAAAAGTGCAGAGCCTGCAT
upper sequence: GLYMA18G12080.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
aataattgtttcaaaaatgttattgatcaatttagtcattctcctttatttatcattttgaatggatgatg-actttagtt--tttgttttgtttctccttcaGGTTGCTGTTGCACATACAATAGGACATGTAGCGGCAACAGTTAGTATGTCAAAAGTTGCGGTATCGTTTACACATATTATCAAGAGTGGTGAACCTGCT-
| | || | | | || | | ||| | | | |||| | | |||||| || || ||| | | ||| | ||| | | | |||||||||| ||||| ||||| || ||||| || ||||| || ||||||||||| ||||| || || || || || || ||||||||||||||||||||
-cttgtcattatatagcttctagtatttcattc---tagtttaaagtattgaactttttgatattttgttgtactgaaagtggtttatgttgaattgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT
upper sequence: GLYMA18G12080.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 1
aataattgtttcaaaaatgttattga--tcaatttagtcattctcctttatttatcattttgaatggatgatgactttagtttttgttttgtttc---tccttcaGGTTGCTGTTGCACATACAATAGGACATGTAGCGGCAACAGTTAGTATGTCAAAAGTTGCGGTATCGTTTACACATATTATCAAGAGTGGTGAACCTGCT-
| | | || | || | | ||| | | | | || | ||||| ||| |||| | | | ||| | | |||||||||| || |||||||| || ||||| || |||||||| |||||||| || |||||||| || ||||| || || |||||||||||||| |||||
------taaattggagttgcttttaaaatggattcccttagttttctcggcagccaaacagagctggattgtgaatttataatcaatctgattttatgttttgtagGTTGCTGTGGCTCATACAATTGGGCATGTGGCTGCAACAGTGAGTATGTCCAAGGTTGCGGTGTCTTTTACTCACATAATCAAGAGTGGTGAGCCTGCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttatcattttgaatggatgatgactttagtttttgttttgtttctccttcaGGTTGCTGTTGCACATACAATAGGACATGTAGCGGCAACAGTTAGTATGTCAAAAGTTGCGGTATCGTTTACACATATTATCAAGAGTGGTGAACCTGCT
ctttagtttttgtttt CT-rich tract
tttagtttttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aataattgtttcaaaaatgttattgatcaatttagtcattctcctttatttatcattttgaatggatgatgactttagtttttgttttgtttctccttcaGGTTGCTGTTGCACATACAATAGGACATGTAGCGGCAACAGTTAGTATGTCAAAAGTTGCGGTATCGTTTACACATATTATCAAGAGTGGTGAACCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg