Sequence
atgc intronic sequence ATGC exonic sequencegttggctcttgtggttacattatgtagttttgtaggttcaatgaagtatgaagatatggaaggtttttgatgtaaagcaagacacctgatgcatcatatttttaccgaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGCTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGGGTAAAGATGGTATCATCCCCTCATCTTATAC
Basic information
species | Glycine max |
transcript | GLYMA18G40600.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G40600.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g38270.2 (Oryza sativa), 3'ss of exon 5
gttggctcttgtggttacattatgtagttttgtaggttcaatgaagtatgaagatatggaaggtttttgatgtaaagcaagacacctgat--gcatcatatttttaccgaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGCTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGGGTAAAGATGGTATCATCCCCTCATCTTATAC-------
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-------------------gtaacttatattgggcgtttactgctgtattc---tcttcacactcaactaggttaggtaagcatgctgatcagcgaaatattttctccaaagctt-cagATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAACTAGGTTTAGGCTCTAGGATCCGGACAGTTTCCTCCCCACATCCCATACCTTGTGT
upper sequence: GLYMA18G40600.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g38270.1 (Oryza sativa), 3'ss of exon 5
gttggctcttgtggttacattatgtagttttgtaggttcaatgaagtatgaagatatggaaggtttttgatgtaaagcaagacacctgat--gcatcatatttttaccgaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGCTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGGGTAAAGATGGTATCATCCCCTCATCTTATAC-
|| | | ||| ||| | || |||| | | | | | || | | ||| ||||| || ||||||| || ||| || ||||| | || ||||||||||||||||||||||| || |||||||| ||||| || || ||| || | || || || ||||| |||| ||||
-------------------gtaacttatattgggcgtttactgctgtattc---tcttcacactcaactaggttaggtaagcatgctgatcagcgaaatattttctccaaagCTT-CAGATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAACTAGGTTTAGGCTCTAGGATCCGGACAGTTTCCTCCCCACATCCCATACC
upper sequence: GLYMA18G40600.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g62810.4 (Oryza sativa), 3'ss of exon 4
gttggctcttgtggt-tacattatgtagttttgtaggttcaatgaagt-atgaagatatggaaggtttttgatgtaaagcaagacacctgatgcatcatatttttaccgaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGCTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGGGTAAAGATGGTATCATCCCCTCATCTTATAC-
|| | |||||| || | | || | | | | || |||| || |||| |||| | | | |||| |||| ||||||| | || || || |||||||||||||||||||| ||||| || ||||| |||||||| | | || || || || || |||| ||| |
----------gtagcctacattttgcactaacactatggcactacatttgctgggctagggaactttgctgat-taaaactaaatg---------------ttttctcgaaagCTTCAGATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCC
upper sequence: GLYMA18G40600.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g62810.3 (Oryza sativa), 3'ss of exon 2
gttggctcttgtggt-tacattatgtagttttgtaggttcaatgaagt-atgaagatatggaaggtttttgatgtaaagcaagacacctgatgcatcatatttttaccgaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGCTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGGGTAAAGATGGTATCATCCCCTCATCTTATAC-------
|| | |||||| || | | || | | | | || |||| || |||| |||| | | | |||| |||| ||||||| | || || || |||||||||||||||||||| ||||| || ||||| |||||||| | | || || || || || |||| ||| |
----------gtagcctacattttgcactaacactatggcactacatttgctgggctagggaactttgctgat-taaaactaaatg---------------ttttctcgaaagcttcagATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCCGTGCAT
upper sequence: GLYMA18G40600.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
gttggctcttgtggttacattatgtagttttgtaggttcaatgaagtatgaagatatggaaggtttttgatgtaaagcaagacacctgatgcatcatatttttaccgaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGCTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGGGTAAAGATGGTATCATCCCCTCATCTTATAC-------
||| | || || | || | || ||| | ||| | | || | | || |||| | | ||||||| | || ||||| ||||||||||| |||||||| ||||| || ||||| ||||||||| | | | || || || || |||| | |||
-------------------------------gtaacctgcatatgtcattatgacactgaca-tttgccctataaggatatttactgactaaaatattttttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
upper sequence: GLYMA18G40600.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G53830.1 (Arabidopsis thaliana), 3'ss of exon 5
gttggctcttgtggttacattatgtagttttgtaggttcaatgaagtatgaagatatggaaggtttttgatgtaaagcaagacacctgatgcatcatatttttaccgaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGCTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGGGTAAAGATGGTATCATCCCCTCATCTTATAC-------
|| ||| || | ||| || ||| |||||| | || | | || |||| ||||| ||||||| ||||||| ||||| | |||||| | ||||||||||| |||||||| ||||| || |||||||||||||| ||| | || ||||| ||||| |||||||| ||||
--------gtgaagttgaataa-acgactttttaca---aatccgagatgaagctgct---accttgtagttgaagattcatttgaggatg-atcatgtttttacggaagttt-cagATTTAGGACAGATTTGGGGTTGGGGATATGGAGGCGAAGGTCAACTAGGATTGGGTTCCCGGATTAAAATGGTGTCATCTCCTCATCTAATACCTTGCCT
upper sequence: GLYMA18G40600.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv08s0007g00930.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------------------gttggctcttgtggttacattatgtagttttgtaggttcaatgaagtatgaagatatggaaggtttttgatgtaaagcaagacacctgatgcatcatatttttaccgaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGCTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGGGTAAAGATGGTATCATCCCCTCATCTTATAC-------
|| ||||||||||| ||| ||||||||||||| ||||||| |||| |||||||| | ||| |||||||||||||||||| || ||| | || |||||||| |||||||||| |||||||||||||||||||| ||||| |||||||| |||||||||||| |||| |||| || || |||||||| ||||
gtaaattctccatcccctgggtcactgcagcccacacaagccacagttttcaggtgtagcaatttcttctttgtggttacactatatagttttgtaggtcatttgaagtacgaagctatggaagatctttaatgtaaagcaagacacctaat-----------ttaacaaaagtttcagATATGGGACAGGTGTGGGGTTGGGGCTATGGAGGCGAAGGGCAGCTAGGTTTGGGTTCTCGGACAAAGCTGGTGTCTTCTCCTCATCTCATACCTTGCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggaaggtttttgatgtaaagcaagacacctgatgcatcatatttttaccgaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGCTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGGGTAAAGATGGTATCATCCCCTCATCTTATAC
acctgat putative branch site (score: 4)
tttttacc putative PPT
atcatattttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggctcttgtggttacattatgtagttttgtaggttcaatgaagtatgaagatatggaaggtttttgatgtaaagcaagacacctgatgcatcatatttttaccgaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGCTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGGGTAAAGATGGTATCATCCCCTCATCTTATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG