Sequence
atgc intronic sequence ATGC exonic sequence...acaaatgtttgggcagagcatcaagcatatgattatgttgcatgattgattgatgtttatatgctactacctgttgtttgactcgaatattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTCGGCAAACCTTTCAATT
Basic information
species | Glycine max |
transcript | GLYMA01G34560.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 7
------acaaatgtt----tgggcagagcatcaagcatatgattatgttgcatgattgattgatgttta-tatgctactacctgttgtttgactcgaatattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTCGGCAAACCTTTCAATT
||| || | |||| | | || | || | | ||||| || | || ||| | || ||| | || | | |||||||| |||||||| |||||||||||||| ||||||||||| |||||||| | |||||||| ||||| || |||||||| || | || || ||||||
gtaagtacagggcttcctatattcagattgcaatgtatttccccatacttt-tctttgatgtatttatagtatataggcagtatatgattgtgtttccctttctcttgtagGCACTACAATATGAATCGCATCAGGCTTGTCTGGTCAAGCATATGGCATGTCTTGTCTGATTTTTTTGTTACAATTGGCTGCTCAGAGAATCTCTCAATT
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 7
---acaaatgtttgggcagagcatca--agcatatgattatgt-------tgcatgattgattgatgtttatatgctactacctgttgtttgactcgaatattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTCGGCAAACCTTTCAATT
| ||| | || | |||| | | || |||| | ||| || | | | ||||| | | | | || | ||| | | | | ||||| || ||||||||||||||||| ||||| |||||||| || |||||||| | |||||||| ||||| || |||||||| || | ||| ||||||||
gtaaggaatctgaggctttattatcattactacattgcaatgtgtttttttacatttctgttcggt-cttatagac-agtgcatgattttttttttttttgccctcttgtagGCATTACAATATGAACCGCATCAGACTTGTTTGGTCAAGTATATGGCATGTCTTGTCTGATTTTTTTGTCACCATTGGCTGCTCAGAAAATCTTTCAATC
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------------------acaaatgtttgggcagagcatcaagcatatgattatgttgcatgattgattgatgtttatatgct-actacctgttgtttgactcgaatattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTCGGCAAACCTTTCAATT
| | |||| | | | | | | | | || | || | || || || | | |||||| | ||| ||| ||||||| ||||| ||||| ||||| |||||||| ||||||||||||||||| || || || | ||||||||| || ||||| || || | || ||||| |||
gtaagaatctcctagtttcgttcctctctgttctctcatatactgcatataagagacgttctctgttcttagcaactttaagtatgtagtctgacaattttctgtttgtc------att-tgtgacagGCATTATAACATGAATCGCATAAGGCTTGTTTGGTCAAGCATCTGGCAAGTGCTATCAGGTTTCTTTGTGACCATTGGATGCTCAGAGAATCTTTCTATT
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 7
acaaatgtttgggcagagcatcaagcatatgattatgttgcatgattgattgatgtttatatgctactacctgttgtttgactcgaatattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTCGGCAAACCTTTCAATT
| | | ||||| | | | ||| | | || || || || | | || || | | || | || | |||||||||||| ||||||||||| || ||||| ||||| |||||||||||||| ||||||||||||||||| |||||||||||||| | ||||| || |||
------------gtaagg-atcaatcttttctttacgatatctgttttgtttttgctcactctctcttatttataccctgtttgttgta----atggcagGCACTATAACATGAACCGCATAAGACTTGTCTGGTCGAGCATCTGGCATGTGCTCTCTGATTTCTTTGTGACTATTGGCTGTTCTGATAACCTCTCCATT
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 7
-------------acaaatgtttgggcagagcatcaagcatatgattatgttgcatgattgattg---atgtttatatgctactacctgttgtttgactcgaatattatgtaa----------------cagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTCGGCAAACCTTTCAATT
||| | | | | | |||||| || | ||| | ||| ||| || ||| | ||| ||| ||| || ||| || || | |||||||||||| |||||||| |||||||||||||||||||||||||||||||| ||||| |||||||||||||| ||||||||||| | ||||||||||||
gtatgaatcattctcaatttgtcttgttcatgttttagcataccatattagtgcttcatttattatttatatttgtcagctgctattaaaaattttgctaaaattctaagtgatttgttttcttttacacagGCACTATAACATGAACCGTATCAGGCTTGTGTGGTCAAGCATCTGGCATGTACTCTCAGATTTCTTTGTAACCATTGGCTGTTCAGAGAACCTTTCAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgattgatgtttatatgctactacctgttgtttgactcgaatattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTCGGCAAACCTTTCAATT
gtttgac putative branch site (score: 4)
aatattatgtaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acaaatgtttgggcagagcatcaagcatatgattatgttgcatgattgattgatgtttatatgctactacctgttgtttgactcgaatattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTCGGCAAACCTTTCAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - gtttggg
- - - - - - - - - - -caagcat
- - - - - - - - - - - - - - - - - - - -gcatgat
- - - - - - - - - - - - - - - - - - - - - - - - - tgatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgttg