Sequence
atgc intronic sequence ATGC exonic sequencegtgaatttcaatcgaatttcaatttgaactttactctcaagtaccgtatcactgtttttattttttatttttatttttgttgatgtagGTTGAGACTGATAGGGAAGCTGGAGGGAACAAAGGTGTGTCTGATAAACAGATTCGTTTGAAGATTTTTTCGCCGAATGTTCTCGACATTACGCTCGTGG
Basic information
species | Glycine max |
transcript | GLYMA08G07160.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G07160.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g31190.1 (Oryza sativa), 3'ss of exon 1
--gtgaatttcaatcgaatttcaatttgaactttactct-caagtaccgtatcactgtttt-tattttttatt--tttatttttgttga------tgtagGTTGAGACTGATAGGGAAGCTGGAGGGAACAAAGGTGTGTCTGATAAACAGATTCGTTTGAAGATTTTTTCGCCGAATGTTCTCGACATTACGCTCGTGG
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gtacttataataatccttcttttttttggttgggggggggtgggtcttgttttatgctttcgtgattcttacgagatgaattatgttgactgtttttcagTTGGAAACGGATAAAGAAGCTGGGGGCAACAAAGGGGTTTCTGAGAAACAGATTCGTCTGAAAATATTTTCACCAAATGTCCTAGACATCACCTTGGTTG
upper sequence: GLYMA08G07160.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G180335_T01 (Zea mays), 3'ss of exon 1
---------------gtgaatttcaatcgaatttcaatttgaactttactctcaagtaccgtatcactgtttttattttttatttttatttttgttgatgtagGTTGAGACTGATAGGGAAGCTGGAGGGAACAAAGGTGTGTCTGATAAACAGATTCGTTTGAAGATTTTTTCGCCGAATGTTCTCGACATTACGCTCGTGG
| | || || | | | || ||| | | | | || | ||| | | | ||| | | | ||| ||| || || || | || || || || ||||||||||| || |||| ||||| || |||||||||||||| || |||||||| ||||||| | || |
tgtttggtattttgtttcacttcttttctttagttagtgtgggcttgagttgccattagtgctccacagaccat---tgttaaaagactctgcatctatgcagGCAGAAACAGACCGAGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAGATACGATTGAAGATTTTTTCTCCAAATGTTCTTAACATTACTTTGGTTG
upper sequence: GLYMA08G07160.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 1
-------gtgaatttcaa---tcgaatttcaatttgaactttactctcaagtaccgtatcactgtttttattttttatttttatttttgttgatgt--agGTTGAGACTGATAGGGAAGCTGGAGGGAACAAAGGTGTGTCTGATAAACAGATTCGTTTGAAGATTTTTTCGCCGAATGTTCTCGACATTACGCTCGTGG
|| |||| | | || | | | |||| || | | | | | | || ||| | || | ||| |||||| |||||||||||||||| ||||||||||| || ||||| ||||||||||| ||||| || ||||| ||||| || || || || || ||||
ttatttttatcatctcaagctttgcatgtataccaaagtaatacttaaaactttgaagatagtttccccccccctcaaaattctttccaatcatcttcagGCTGAGACAGATAGGGAAGCTGGAGAAAACAAAGGTGTTTCAGATAAGCAGATTCGTTTAAAGATATTCTCGCCAAATGTCCTTGATATCACACTAGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctcaagtaccgtatcactgtttttattttttatttttatttttgttgatgtagGTTGAGACTGATAGGGAAGCTGGAGGGAACAAAGGTGTGTCTGATAAACAGATTCGTTTGAAGATTTTTTCGCCGAATGTTCTCGACATTACGCTCGTGG
tgttgat putative branch site (score: 4)
tttttattttttattt CT-rich tract
tatcactgtttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaatttcaatcgaatttcaatttgaactttactctcaagtaccgtatcactgtttttattttttatttttatttttgttgatgtagGTTGAGACTGATAGGGAAGCTGGAGGGAACAAAGGTGTGTCTGATAAACAGATTCGTTTGAAGATTTTTTCGCCGAATGTTCTCGACATTACGCTCGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA