Sequence
atgc intronic sequence ATGC exonic sequencegtaagggttttctgggttttatctttgtttttattattttgttgcaagattgatggattatataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
Basic information
species | Glycine max |
transcript | GLYMA07G38050.2 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
gtaagggttttctgggttttatctttgtttttattattttgttgcaag-attgatggatta-tataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
| ||||| || | | | |||| || | | | ||| ||| | || || | |||| || | || | | ||||||| ||||| ||||| || | |||||||| ||||||||||| |||||||| || |||||||||||||| |||||||||||||||||||||||| | ||
-----------gtatgtttttgctgcttgtattttatgtttaagaaggcattcatgcagtagtaagatatggatttattttgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
gtaagggttttctgggttttatctttgtttt-tattattttgttgcaagattgatggattatataacatggtacaatctatttgtgta----tgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
||| | |||| || || || ||| | | | ||| | | | | || | ||| | || | ||||||| ||||| |||||| | | || ||||| |||||||||||||||||||| || || |||||||| || ||||| |||||||| ||||||||| | ||
---------------gttagttttttgcttcataaaatgttgcttgacaaatgaaaattcaaacatcaattaatgttcttctgtcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 10
gtaagggttt----tctgggttttatctttgtttttattattttgttgcaagattgatggattatataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
||| || ||| | || ||| | |||||||| | ||||| || | || ||||| | || | |||| | | | ||| |||||| ||||| ||||| | || |||||||| | |||||||||||||||||||| ||||| |||||||| ||||| || |||||||| |||||| | ||
gtatggttttgatatttgccatttctatttgttttaagcatttt-ttactagtttgat---ctggattgttctg-acaacattctcatttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 13
-----gtaagggttttctgggttttatctttgtttttattattttgttgcaagattgatggattatataacatggt-acaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
|| | | | || || ||| | ||||||| | ||||| | | | | | ||| | || | |||| | || | | | |||||| ||||| ||||| | || |||||||| | |||||||||||||||||||| ||||| |||||||| ||||| || |||||||| |||||| | ||
gtatggttatgatatt-tgcctttgctatttgtttcaagcatttttcttta---ctagttggatatggattattctgacaacattcttttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaagggttttctgggttttatctttgtttttattattttgttgcaagattgatggattatataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
| | | | | ||| ||| | | || || | | | || ||||| | || ||||||||||| ||||| |||||||||||||||||||| |||| ||||||||| ||||| || ||||| || || || ||||| ||||| ||||||||||| |||||
-------------gtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaat-tggtat--ttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaagggttttctgggttttatctttgtttttattattttgttgcaagattgatggattatataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
||||| | || | || | | ||| | | ||| | | | |||||| || | | | |||| | | ||||||| ||||| |||||||||||||||||||| |||| ||||||||||||||| |||||||| || || || |||||||| ||||||||||||||||||||
gtaagtgcttg------tgtactgaggctgtta--gatgtattggattttctcttacatatatatactgatttcttttctttgc-tttccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 13
gtaagggttttctgggttttatctttgtttt-tattattttgttgcaagattgatggattata-----taacatggtacaatctatttgtg--tatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
|| || |||||| || | ||| ||| | ||| | || | | | | || | |||||| | | | | || | | ||||||||| || ||||||||| | || |||||||| || |||||||||||||||||||| || |||||||| || |||||||| ||||| || || ||||| ||
gtgagccatttctgcattacaagcttgctttgcactatgacat-gctaattcatagaactagaaccactaacattttgttgtttttgtgggcttttgcagCTGTGAACAAAGATGAGCTACTGCAAATGGTCAGGTTTGGTGCTGAAATGGTTTTCAGCTCCAAGGATAGCACAATTACGGATGAAGACATAGACAGGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgttgcaagattgatggattatataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
atataac putative branch site (score: 3)
attatataacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagggttttctgggttttatctttgtttttattattttgttgcaagattgatggattatataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT