Sequence
atgc intronic sequence ATGC exonic sequence...tttctaaaaactattttcaagtgagatagcaccactgatttacacattgattaattattcagttattggtgcatgattggtaaaatatgtgttattgcagTGTTTTATAGTGAGCACAGTCAATGCTTTGCAGACACCAATGATCAATGCTGCCATG
Basic information
species | Glycine max |
transcript | GLYMA10G10990.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G10990.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g36440.1 (Oryza sativa), 3'ss of exon 4
tttctaaaaactattttcaagtgagatagcaccactgatttacacattgattaattattcagttattggtgcatgattggtaaaatatgtgttattgcagTGTTTTATAGTGAGCACAGTCAATGCTTTGCAGACACCAATGATCAATGCTGCCATG
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---gtgtgagatatttgtgagtttactcacttgttcaattttt-ctttcgtcgaccatgtgattctctgttaac-accagtttattcactttgtttgtagTGCTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATTAATGCAAGCATG
upper sequence: GLYMA10G10990.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G108457_T02 (Zea mays), 3'ss of exon 4
tttctaaaaactattttcaagtgagatagcacc---actgatttacacattg--attaattattcagttattggtgcatgattggtaaaatatgtgttattgcagTGTTTTATAGTGAGCACAGTCAATGCTTTGCAGACACCAATGATCAATGCTGCCATG
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---gtgtgagagatttgtgagttgactcactttttaagcattccatcttctgtcaatactggtttagttgaagactcatgattattaat-----tgtt-ttgtagTGTTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATAAATGCAAGCATG
upper sequence: GLYMA10G10990.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G106531_T01 (Zea mays), 3'ss of exon 4
----------tttctaaa--aact--attttcaagtg-----agatagcaccactgatttacacattgattaattattcagttattggtgcatgattggtaaaatatgtgttattgcagTGTTTTATAGTGAGCACAGTCAATGCTTTGCAGACACCAATGATCAATGCTGCCATG
||| | | ||| ||||||||| | | || |||| | || | | || | || ||| | || ||||||| ||| | | ||| |||||||||| ||||||||||||||||| ||||| ||||| ||||| ||||| ||||
gtatgagagatttgtgagttgactcacttttcaagttttcctctttggagcctgtgatcttcag--tcaatactagtttagtgaaaagttcatgattattaat-----tatctttgtagTGTTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATAAATGCAAGCATG
upper sequence: GLYMA10G10990.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G06820.1 (Arabidopsis thaliana), 3'ss of exon 4
-tttctaaaaactatt--ttcaagtgagatagcaccactgatttacacattgattaattattcagttattggtgcatgattggtaaaatatgtgttattgcagTGTTTTATAGTGAGCACAGTCAATGCTTTGCAGACACCAATGATCAATGCTGCCATG
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gtgagaaaaaaacattattttttcttaacttgcacaattt-ttttcactcaaatttat-atccagaatatagcatggatatcacccttcatatttgcctgcagTGTTTCATTGTGAGCACAGTCAATGCTTTGCAGACGCCAATGATCAATGCAAGTATG
upper sequence: GLYMA10G10990.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0032g00800.t01 (Vitis vinifera), 3'ss of exon 4
------------tttctaaaaactattttcaagtga-----gatagcaccactg--atttacacattgattaattattcagttattggtgcatgattggtaaaatatgtgttattgcagTGTTTTATAGTGAGCACAGTCAATGCTTTGCAGACACCAATGATCAATGCTGCCATG
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gtttgccgcagttatttcatagttgatgttgagtttttcttattgatagctttggaaccttcatatggcatatcccactactttcatgagcatcaatgttaactatggtatgtctgcagTGTTTTATAGTGAGCACAGTTAATGCTTTGCAGACACCAATGATCAATGCGAGCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgattaattattcagttattggtgcatgattggtaaaatatgtgttattgcagTGTTTTATAGTGAGCACAGTCAATGCTTTGCAGACACCAATGATCAATGCTGCCATG
gattaat putative branch site (score: 3)
ttaattattcagttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttctaaaaactattttcaagtgagatagcaccactgatttacacattgattaattattcagttattggtgcatgattggtaaaatatgtgttattgcagTGTTTTATAGTGAGCACAGTCAATGCTTTGCAGACACCAATGATCAATGCTGCCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - taaaaac
- - - - - - - - -caagtga
- - - - - - - - - - - - - - gcaccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgat