Sequence
atgc intronic sequence ATGC exonic sequence...tgaaatggaaccaaattttccctttgcatttttcctgcaatatatgttttctaattctatacacctatttttaactaggtactactactttacattttagGTATTCTGCAAGGCTTACAGACAGGTTGATCCTTGTGTTCATTCAAGTATGAAACATCTTTTTGGAACTTGGAAAGGAGTCTTTCCTCCTCAGTCCCTTC
Basic information
species | Glycine max |
transcript | GLYMA19G37600.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G37600.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G142168_T01 (Zea mays), 3'ss of exon 4
----------------------------------tgaaatggaaccaaattttccctttgca--------tttttcctgcaatatatgttttctaattctatacacctatttttaactaggtactactactttacattt--tagGTATTCTGCAAGGCTTACAGACAGGTTGATCCTTGTGTTCATTCAAGTATGAAACATCTTTTTGGAACTTGGAAAGGAGTCTTTCCTCCTCAGTCCCTTC
| || || | | || || | || || | | ||| || | || | | ||| ||| | ||| || | || | ||| ||||| ||||||||||| || | ||| |||||||||| | | ||| || |||| |||||||||||||| ||||||||||| ||||||| | | || |
gttagtatttcattttgcaccatcttcttgacatgggaacagagatggttcctacccctggaaaccatatttatttattgagaggatgacttggacatcacaataactaagttttctttggttgtatt-tttcatttttgctagGTGTTCTGCAAGGCATATAAACAAGTTGATCCTTCTATACATCATAGCATGAGGCATCTTTTTGGAACATGGAAAGGAGTGTTTCCTCTACCTCCTCTCC
upper sequence: GLYMA19G37600.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G36480.3 (Arabidopsis thaliana), 3'ss of exon 1
tgaaatggaaccaaattttccctttgcatttttcctgcaatatatgttttctaattcta-tacacctatttttaactaggtactactactttacattttagGTATTCTGCAAGGCTTACAGACAGGTTGATCCTTGTGTTCATTCAAGTATGAAACATCTTTTTGGAACTTGGAAAGGAGTCTTTCCTCCTCAGTCCCTTC
| | || | | | | | ||||||| | | ||| | | || | | | | || | || | | |||| || ||||||||||| || ||||| ||| | | ||||| | ||| |||||||||||||| |||||||||||||||| ||| || | ||||
---------gtttggtgctttgttgatagtcatggt-tatagaatgtttttt--tcctagcaaattcatctctgatcaccctctttttactt-ctctgaagGTTTTTGTTAAGGCTTACAGGCAAGTTGACCCTCCTATGCATTCTAACATGCGGCATCTTTTTGGAACCTGGAAAGGAGTCTTTCATCCGCAAACACTTC
upper sequence: GLYMA19G37600.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g03880.t01 (Vitis vinifera), 3'ss of exon 2
-tgaaatggaaccaaattttccctttgcatttttcctgcaatatatgttttctaattctat--acacctatttttaactaggtac-tactactttacattttagGTATTCTGCAAGGCTTACAGACAGGTTGATCCTTGTGTTCATTCAAGTATGAAACATCTTTTTGGAACTTGGAAAGGAGTCTTTCCTCCTCAGTCCCTTC
| || | | | |||||| || || | ||| || || |||| | | | || ||| | | || ||| ||| | | ||||||||||||||||| || ||||| |||||||||| | | ||| | ||||| |||||||||||||| ||||||||||| || |||| | | ||||
agtagatatcattgcaatgcatctttgctttgtttatctgctat----ttcctgattccactaatatctcactttggtttgtaacctacctttttttactctagGTATTCTGCAAGGCATATAGACAAGTTGATCCTTCTATACATCCTGGTATGCGGCATCTTTTTGGAACGTGGAAAGGAGTGTTCCCTCTTGCACCACTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttctaattctatacacctatttttaactaggtactactactttacattttagGTATTCTGCAAGGCTTACAGACAGGTTGATCCTTGTGTTCATTCAAGTATGAAACATCTTTTTGGAACTTGGAAAGGAGTCTTTCCTCCTCAGTCCCTTC
ttttaac putative branch site (score: 2)
ctacttt putative PPT
tactttacatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaaatggaaccaaattttccctttgcatttttcctgcaatatatgttttctaattctatacacctatttttaactaggtactactactttacattttagGTATTCTGCAAGGCTTACAGACAGGTTGATCCTTGTGTTCATTCAAGTATGAAACATCTTTTTGGAACTTGGAAAGGAGTCTTTCCTCCTCAGTCCCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - aaccaaa
- - - - - - - - - - cctttgc
- - - - - - - - - - - - - - - - tcctgca