Sequence
atgc intronic sequence ATGC exonic sequencegtatctgaaaagtgtaacacaataactgtttgcttgagccttgaatgtcatcgctcttattatttaacataattgcaacttttctaaacaacagtgctttctatgttttaacagTTGATGTTTTTGCTGATGCATCATCAATGGTAATCTCTGTACTGGATGGCTACAATGTTTGCATCTTTGCTTATGGACAAACAGGAACAGGGAAGACATT
Basic information
species | Glycine max |
transcript | GLYMA09G33340.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G33340.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g02290.2 (Oryza sativa), 3'ss of exon 1
-------------------------------------------------gtatctgaaaagtgtaacacaataactgtttgcttgagccttgaatgtcatcgctcttattatttaacataattgcaacttttctaaacaacagtgc---tttctatgttttaacagTTGATGTTTTTGCTGATGCATCATCAATGGTAATCTCTGTACTGGATGGCTACAATGTTTGCATCTTTGCTTATGGACAAACAGGAACAGGGAAGACATT
|| || | | | ||| || | || | || | || || || |||| ||| | || | | | | || |||| | | ||| |||||| | ||| |||||||| || |||| | || || |||||||||||||||| ||||| ||||| || ||||||||||||||||||||||| ||
gtatttctaactatgctggagtttctattgggcctctttgtcctttacagttcttgtgtttttttagacatgaaagatcaaaatggtagctctataatgt-gcagctagtaattaaagcaatggtgcattataacatctaatctgtaaatttccaataatgtgcagCTGATGTGTATGCCGATGCATCTCCACTGGTTACTTCGGTCTTGGATGGCTACAATGTGTGCATATTTGCGTACGGACAAACAGGAACAGGGAAGACTTT
upper sequence: GLYMA09G33340.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G092232_T01 (Zea mays), 3'ss of exon 7
gtatctgaaaagtgtaacacaataactgtttgcttgagccttgaatgtcatcgctcttattatttaacataattgcaacttttctaaacaacagtgctttctatgttttaacagTTGATGTTTTTGCTGATGCATCATCAATGGTAATCTCTGTACTGGATGGCTACAATGTTTGCATCTTTGCTTATGGACAAACAGGAACAGGGAAGACATT
| | | | || ||| | |||| | || |||| || | ||| | | || | | | || ||||| || || || | ||||| | ||| | ||| ||||| || || | || | ||||| | |||||||||||||| |||||||||||||| ||||| || |||||||| ||||| ||
-tgttttttttctaaaaagcaagag-----tgct--aatctattatgt--tcaaacaacttaccttatatgacttctg-ttgtctaatatgcaac---ttgaattaatgaacagATATTGTGTATGCCGATGCGTCTCCACTAGTCACATCTGTCTTAGATGGCTACAATGTATGCATCTTTGCTTACGGACAGACGGGAACAGGAAAGACTTT
upper sequence: GLYMA09G33340.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G22610.2 (Arabidopsis thaliana), 3'ss of exon 9
gtatctgaaaagtgtaacacaataactgtttgcttgagccttgaatgtcatcgctcttattatttaacataattgcaacttttctaaacaacagtgctttctatgttttaacagTTGATGTTTTTGCTGATGCATCATCAATGGTAATCTCTGTACTGGATGGCTACAATGTTTGCATCTTTGCTTATGGACAAACAGGAACAGGGAAGACATT
| |||| | | || | | || | ||||| |||| | ||| || ||||| | || ||| |||| | |||||||||| || || ||||| || | ||||| | || || || || |||||||||||||| || ||||| || ||||||||||||||||| ||||| ||
------------------------gtagcgtgct-atgtcatggtcaagttagatcattaagtttaa-ataacagtaacaatt---aacaaagtttctatctttgttgtg-cagTTGATGTCTTCGCCGATGCTTCTCCGATGGTTGTTTCAGTCCTAGACGGCTACAATGTTTGTATTTTTGCCTACGGACAAACAGGAACAGGAAAGACGTT
upper sequence: GLYMA09G33340.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv00s0218g00050.t01 (Vitis vinifera), 3'ss of exon 9
gtatctgaaaagtgtaacacaataactgtttgcttgagccttgaatgtcatcgctcttattatttaacataattgcaacttttctaaacaacagtgctttctatgttttaacagTTGATGTTTTTGCTGATGCATCATCAATGGTAATCTCTGTACTGGATGGCTACAATGTTTGCATCTTTGCTTATGGACAAACAGGAACAGGGAAGACATT
|||| || ||| | | | || | | |||| ||||| | | ||| | ||| | | ||| ||| |||||||||||||| ||||| ||||| ||| ||||||| || || || | ||||| |||||||| || || ||||| ||||| |||||||| ||||| ||||||||
-----------gtgtgcatatattactactaattgg-----tggaca----cagtcttgctattttaact--ttgtgaactttgcattaagtgagaattttcttgtcttaacagTTGATGTGTTTGCGGATGCGTCACCAATGGTGATTTCAGTGTTAGATGGATACAATGTCTGTATATTTGCATATGGGCAAACAGGCACAGGAAAGACATT
upper sequence: GLYMA09G33340.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ04247 (Selaginella moellendorffii), 3'ss of exon 8
gtatctgaaaagtgtaacacaataactgtttgcttgagccttgaatgtcatcgctcttattatttaacataattgcaacttttctaaacaacagtgctttctatgttttaacagTTGATGTTTTTGCTGATGCATCATCAATGGTAATCTCTGTACTGGATGGCTACAATGTTTGCATCTTTGCTTATGGACAAACAGGAACAGGGAAGACATT
| | ||| | || | | | | || || | | || | || ||| ||| || ||||| || | || | | || | ||||| |||||||||||||| || ||||| ||||| || ||||||||||| || || || |||||
-------------------------------------------------------gtgagtatatggcaaagt--ctatattcacaagc--tgatcctcgtttccgttgtgcagCTGAAGTGTTTGCAGACACGTCTCCGGTCGTTGTATCTGTCCTGGATGGCTACAACGTGTGCATATTTGCCTACGGACAAACAGGTACTGGCAAAACATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttaacataattgcaacttttctaaacaacagtgctttctatgttttaacagTTGATGTTTTTGCTGATGCATCATCAATGGTAATCTCTGTACTGGATGGCTACAATGTTTGCATCTTTGCTTATGGACAAACAGGAACAGGGAAGACATT
ttctaaa putative branch site (score: 2)
tttctatgttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctgaaaagtgtaacacaataactgtttgcttgagccttgaatgtcatcgctcttattatttaacataattgcaacttttctaaacaacagtgctttctatgttttaacagTTGATGTTTTTGCTGATGCATCATCAATGGTAATCTCTGTACTGGATGGCTACAATGTTTGCATCTTTGCTTATGGACAAACAGGAACAGGGAAGACATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA