Sequence
atgc intronic sequence ATGC exonic sequence...aaacaaagttttactattatcaaggagctctgctgacatgtttctaccttggttttgatgactagaatattgttcgcttaaactatttttggactcccagGTGGTGCTTTAAAGCCGACAGATGTTGACACATTGTGGGTTCATGTCACTTGTGCTTGGTTTCGACCTGAAGTCTCTTTTGCTAGTGATGAGAAGATGGA
Basic information
species | Glycine max |
transcript | GLYMA04G41500.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G170412_T01 (Zea mays), 3'ss of exon 12
---aaacaaagttttactattatcaaggagctctgctgacatgtttctaccttggttttgatgactagaatattgttcgcttaaactatttttggactccc--agGTGGTGCTTTAAAGCCGACAGATGTTGACACATTGTGGGTTCATGTCACTTGTGCTTGGTTTCGACCTGAAGTCTCTTTTGCTAGTGATGAGAAGATGGA
| | ||| | ||| | || | |||| | | || | | |||| || | || || || || | |||| ||| |||||||||||| ||||| ||| ||||||| | ||||||||||| || || ||||| ||||||| | | || ||||||||||||||||| |||||
tcaattctggatttcaatatctgggtgcagtt-tgctctctttttattgagtattttttaatcatta--atcctggcacct--ggtgaactttgaactattgtagGTGGTGCTTTGAAGCCAACAAATGTTGATAACTTGTGGGTTCACGTGACATGTGCATGGTTTCAGTCACAGGTTGCTTTTGCTAGTGATGAGCTCATGGA
upper sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 13
lower sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 12
aaacaaagttttactattatcaaggagctctgctgacatgtttctaccttggttttgatgactaga-atattgttcgcttaaactatttttggactccc---agGTGGTGCTTTAAAGCCGACAGATGTTGACACATTGTGGGTTCATGTCACTTGTGCTTGGTTTCGACCTGAAGTCTCTTTTGCTAGTGATGAGAAGATGGA
| |||| | | |||| | | |||| || || | || |||| | | | |||| || ||| ||| ||||| || ||||| || ||||| || || |||||||||||||| || ||||||||||||| |||||||| | |||||| ||||| || || |||||
----gtggctttataaagtatattcagcttt-ttcacataaacatatggcaccactgcctattaactatatccattggctccgctatgttgtcactgatgatagGAGGTGCATTGAAGCCAACTGATGTGGAAACGTTGTGGGTTCATGTGACATGTGCTTGGTTTCAGCCTGAAGTATGTTTTGCAAGTGAGGAAAAAATGGA
upper sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 13
lower sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 12
---aaacaaagttttactatta--tcaaggagctctgctgacatgtttctaccttggttttgatgactagaatattgttcgcttaaactatttttggactcccagGTGGTGCTTTAAAGCCGACAGATGTTGACACATTGTGGGTTCATGTCACTTGTGCTTGGTTTCGACCTGAAGTCTCTTTTGCTAGTGATGAGAAGATGGA
| | | ||| | | | || || | | | || | ||| | | ||| | || | ||| ||| || | | | || ||| ||||| |||||||| || ||||| || ||| |||||||||| || || ||||||||||||| |||||||| | |||||| ||||| || || |||||
tattagctatcctttcccctcagatcttatagttttaccgagaaattt-tgcattgttgcccatcaactaaat-ttgccaattt---ttgtgtactgataaatagGAGGTGCATTAAAGCCAACTGATGTGGAGACACTGTGGGTTCACGTGACATGTGCTTGGTTTCAGCCTGAAGTATGTTTTGCAAGTGAAGAAAAAATGGA
upper sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv16s0098g00350.t01 (Vitis vinifera), 3'ss of exon 13
aaacaaagttttactattatcaaggagctctgctgacatgtttctaccttggtt-ttgatgacta-gaatattgttcgcttaaact--------atttttggactcccagGTGGTGCTTTAAAGCCGACAGATGTTGACACATTGTGGGTTCATGTCACTTGTGCTTGGTTTCGACCTGAAGTCTCTTTTGCTAGTGATGAGAAGATGGA
|| | ||| | ||| | || || || || || ||| ||| || | ||| ||| || | || | | ||| ||| |||||||||| ||||||| || ||| |||| ||||| |||||||||||||||||||||||||||| ||||||||| ||||| | |||||||| ||||||||
---cagaatttc-----tttcaggagtttcctttggtttggag--actttagttactgacaacgaagaacattctttgattttttttgtggttaaatttctttctcttagGTGGTGCTCTAAAGCCAACTGATATTGAGACATTATGGGTTCATGTCACTTGTGCTTGGTTTCAACCTGAAGTTTCTTTCTCAAGTGATGAAAAGATGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accttggttttgatgactagaatattgttcgcttaaactatttttggactcccagGTGGTGCTTTAAAGCCGACAGATGTTGACACATTGTGGGTTCATGTCACTTGTGCTTGGTTTCGACCTGAAGTCTCTTTTGCTAGTGATGAGAAGATGGA
ttttgat putative branch site (score: 4)
ctccc putative PPT
ttaaactattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaacaaagttttactattatcaaggagctctgctgacatgtttctaccttggttttgatgactagaatattgttcgcttaaactatttttggactcccagGTGGTGCTTTAAAGCCGACAGATGTTGACACATTGTGGGTTCATGTCACTTGTGCTTGGTTTCGACCTGAAGTCTCTTTTGCTAGTGATGAGAAGATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
aaacaaa
- - - - - - - - - - - - - -ctctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgac