Sequence
atgc intronic sequence ATGC exonic sequence...tgtgtcttacactcagattattttgatacacctagaatttgtttagtttgtgataaaaaatggagtctgatgaatttttatacgattttggtgctatcagGGCAGTCTCAGCCACCATGCCACCTTTCAGTGTTTCTTGAAGTTACTGATTCAAGAAATACTTCCAGTGATTGGAGTTGTTTTGTAAGTCATCGTTTGTC
Basic information
species | Glycine max |
transcript | GLYMA04G06960.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G06960.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G004908_T01 (Zea mays), 3'ss of exon 1
tgtgtcttacactcagattattttgatacacctagaatttgtttagtt-tgtgataaaaaatggagtctgatgaatttttatacg-attttggtgctatcagGGCAGTCTCAGCCACCATGCCACCTTTCAGTGTTTCTTGAAGTTACTGATTCAAGAAATACTTCCAGTGATTGGAGTTGTTTTGTAAGTCATCGTTTGTC
|| | | | | ||||| || | || || | | | || | || || | | || | || ||| ||| | ||||||||||||| || ||||||||||| ||||||||||| |||||||| ||| | ||||||| | | ||| |||||||| ||||| || |||||| | ||
-gtagcatg-agtatgattacttgtcaatgttgcacatgtgggcattcatacaattgggtactgatccttttacttggttttgtttatgttgctgcaaccagGGCAGTCTCAACCGCCATGCCACCTGTCAGTGTTTCTGGAAGTTACAGATCCCCGAAATACAACTACTGAATGGAGTTGCTTTGTGAGCCATCGTCTCTC
upper sequence: GLYMA04G06960.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G25330.1 (Arabidopsis thaliana), 3'ss of exon 1
-tgtgt---cttacactcagattattttgatacacctagaatt----tgtttagtttgtgataaaaaatggagtctgatgaatttt-----tatac---gattttggtgctatcagGGCAGTCTCAGCCACCATGCCACCTTTCAGTGTTTCTTGAAGTTACTGATTCAAGAAATACTTCCAGTGATTGGAGTTGTTTTGTAAGTCATCGTTTGTC
| ||| | ||||| ||||| | | | || || || ||||| | || | | | || ||| | | || || | ||| | ||| || | ||||||||||| ||||||||| |||| ||||| | ||||||||||| || |||||| ||| || |||||||||||||||||||| || || || | ||
gtatgtaagttcacact-agatt-tctcattgcatcttatgttatgctgttttatatggtagagactataatgtcggttttatattgttgttgtaccttactcttgatggtctcagGGCAGTCGCAGCCACCAAGCCATCTTTCTATATTTCTTGAAGTGACAGATTCACGAAGCTCTAGTAGTGATTGGAGTTGTTTTGTTAGCCACCGACTATC
upper sequence: GLYMA04G06960.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G25320.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------------------------------------tgtgtcttacactcagattattttg---atacacctagaatttgtttagtttgtgataaaaaatggagtctga-tgaatttttatacgattttggtgctatcagGGCAGTCTCAGCCACCATGCCACCTTTCAGTGTTTCTTGAAGTTACTGATTCAAGAAATACTTCCAGTGATTGGAGTTGTTTTGTAAGTCATCGTTTGTC---
| | | | || | || | | || | ||| | ||||| | |||| ||||| || | ||| | || || ||||||||||| |||||||||||||| |||||||| ||||||||||| || |||||| ||| || ||||||||||| |||||||| || || || | ||
gtatgtaagtgtactagattatctgttttatacggtagacatggaaccaacaatctccttttcaatattctgtttttccttcctatgagctgtctgattgctgcatttgtagtgttgaatg---tctgaactgatggtcttac--tcttaatggcctcagGGCAGTCCCAGCCACCATGCCATCTTTCAGTATTTCTTGAAGTGACAGATTCACGAAGC---TCAAGTGATTGGAGCTGTTTTGTTAGCCACCGACTATCAGT
upper sequence: GLYMA04G06960.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0008g05690.t01 (Vitis vinifera), 3'ss of exon 1
---tgtgtcttacactcagattatt--ttgatacacctagaatttgtttagtttgtgataaaaaatggagtctgatgaatttttatacgattttggtgctatcagGGCAGTCTCAGCCACCATGCCACCTTTCAGTGTTTCTTGAAGTTACTGATTCAAGAAATACTTCCAGTGATTGGAGTTGTTTTGTAAGTCATCGTTTGTC
| |||| || || | | |||| | | | | | || || | | || | |||||||| | || | ||| || | ||||||||||||||||||||||||||||||||||| ||||| || ||||| |||||| ||||||||||||||||||||||||||||||| || || || |||||
cttctcattttaccctgaggatttccattgagtctttttgtgctagactaccagttgcttaggaaagtgacctgatgaaccct-atgc----ttgatggtttcagGGCAGTCTCAGCCACCATGCCACCTTTCAGTCTTTCTCGAGGTTACAGATTCACGAAATACTTCCAGTGATTGGAGTTGTTTTGTGAGCCACCGATTGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgtgataaaaaatggagtctgatgaatttttatacgattttggtgctatcagGGCAGTCTCAGCCACCATGCCACCTTTCAGTGTTTCTTGAAGTTACTGATTCAAGAAATACTTCCAGTGATTGGAGTTGTTTTGTAAGTCATCGTTTGTC
gtctgat putative branch site (score: 4)
aatttttatacgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgtcttacactcagattattttgatacacctagaatttgtttagtttgtgataaaaaatggagtctgatgaatttttatacgattttggtgctatcagGGCAGTCTCAGCCACCATGCCACCTTTCAGTGTTTCTTGAAGTTACTGATTCAAGAAATACTTCCAGTGATTGGAGTTGTTTTGTAAGTCATCGTTTGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - -tacactc
- - - - - - - - - - - - - - - - - - - - - - -gtttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagtctg