Sequence
atgc intronic sequence ATGC exonic sequence...aatagtgcttgacttactctattgttactatggttctttgtcttttctttaattcatacttaaaaaattcaatgccataatgaaaagtctgctgtaccagCATGGATGGAAAATATATTTTGACGGGAGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGACACAAC
Basic information
species | Glycine max |
transcript | GLYMA10G05890.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G05890.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 8
------------------------------------aatagtgcttgacttactctattgttactatggttctttgtcttttctttaattcatacttaaaaaa---ttcaatgccataatgaaaagtctgctg-taccagCATGGATGGAAAATATATTTTGACGGGAGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGACACAAC
||| | || || | | | | | || | ||| | || | | || | | || | || ||| ||| || | ||| ||||||||||| || |||||||| ||||| || ||||||||||||||||| ||||||||||| ||||| || |||||||| |||||||||||||| ||
gtgatgggttataattcctttggcaacttttcttataattgaattt-acaaaagttgtcttaaatagataccagtgttgtgagcatatcacccccgtatgatactgtttattgacattgtgattgtattgacactgacagTATGGATGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAAT
upper sequence: GLYMA10G05890.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G37160.1 (Arabidopsis thaliana), 3'ss of exon 8
------------------------------------------------------aatagtgct-tgacttactctattgttactatggttctttgtcttttctttaattcatacttaaaaaattcaatgccataatgaaaagtctgctgtaccagCATGGATGGAAAATATATTTTGACGGGAGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGACACAAC
|||| | | || ||| | | || | || ||| || | | | || || |||| | |||| ||| | || | ||| ||||||||||| || ||||||| ||||| || ||||| || |||||||| ||||||||||||||||| |||||||||||||||||||||||||||||
gtaactggatctaaatcctttgacaaatgatcttccctattgcatttgtaggaaaataatattctgtgttaattttttctccctcaagttgcttttagcatgcgttgttaatttgtaaa----tgtatgc--taacattgcgattggcctgacagTATGGATGGAAAGTACCTTTTGACTGGAGGTGAAGATGACTTGGTTCAAGTGTGGAGTATGGAAGATCGAAAGGTTGTGGCATGGGGTGAGGGACACAAT
upper sequence: GLYMA10G05890.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv08s0040g01960.t01 (Vitis vinifera), 3'ss of exon 8
aatagtgcttgacttactctattgttactatggttctttgtcttttctttaattcatacttaaaaaattcaatgccataatgaaaagtctgctgt--accagCATGGATGGAAAATATATTTTGACGGGAGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGACACAAC
| | | | || |||| | | | | || | | | | ||| | | | ||| | | ||| || | || || | |||| |||||||||||||||||||||| ||||| ||||||||| |||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
-acatgatatcatttcttctagt-tctttttccttttgtaaaatattattactccctttgaaaagagagtggtataatagacaacaaaatgatgctgaacagCGTGGATGGAAAATATATTTTGACTGGAGGTGAGGATGATCTAGTTCAAGTTTGGAGTATGGAAGATCGGAAGGTTGTGGCATGGGGTGAGGGACACAAC
upper sequence: GLYMA10G05890.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ38679 (Selaginella moellendorffii), 3'ss of exon 8
aatagtgcttgacttactctattgttactatggttctttgtcttttctttaattcatacttaaaaaattcaatgccataatgaaaagtctgctgtaccagCATGGATGGAAAATATATTTTGACGGGAGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGACACAAC
| | | | ||| | || | || | | | | || || | ||| |||||| || || | ||| | || ||||||||||||||||| ||||| ||||| |||||||| || |||||| || ||||| ||||| |||||
-----------------------------gtaaacagcgcttgtgtatttggaatacttttcttatatcttctctcttctt------tcctctctcttagCTCGGATGGGAAGTACGTGTTGGCTGGTGGAGAGGATGATTTAGTCCAAGTCTGGAGCATGGAAGACCGGGCGGTTGTTGCCTGGGGAGAGGGTCACAAT
upper sequence: GLYMA10G05890.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ31470 (Selaginella moellendorffii), 3'ss of exon 8
aatagtgcttgacttactctattgttactatggttctttgtcttttctttaattcatacttaaaaaattcaatgccataatgaaaagtctgctgtaccagCATGGATGGAAAATATATTTTGACGGGAGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGACACAAC
| | | | | ||| | || | || | | | | ||| || | ||| |||||| || || | ||| | || ||||||||||||||||| ||||| ||||| |||||||| || |||||| || ||||| ||||| |||||
-----------------------------gtaaacagtgcttgtgtatttggaatacttttcttatatcttctctcttctt------tcttctctcttagCTCGGATGGGAAGTACGTGTTGGCTGGTGGAGAGGATGATTTAGTCCAAGTCTGGAGCATGGAAGACCGGGCGGTTGTTGCCTGGGGAGAGGGTCACAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttaattcatacttaaaaaattcaatgccataatgaaaagtctgctgtaccagCATGGATGGAAAATATATTTTGACGGGAGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGACACAAC
ctttaat putative branch site (score: 4)
aattcatacttaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatagtgcttgacttactctattgttactatggttctttgtcttttctttaattcatacttaaaaaattcaatgccataatgaaaagtctgctgtaccagCATGGATGGAAAATATATTTTGACGGGAGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGACACAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - -tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgcc