Sequence
atgc intronic sequence ATGC exonic sequence...ttggtgttcaattttggccagtccttttggattttctacatggtgaagctaaactaatttatggttttttccaccttttttttttttttttgtacaaaagATATAGGTCTGACCGGGACAAAACTAGGATGTGGGGAAGGTGGTTGTGGAGCTTGCACAGTTATGGTTTCTCAATTTGATAGAAGATTGAAGAAATGCTC
Basic information
species | Glycine max |
transcript | GLYMA15G03870.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G03870.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G34900.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------------------ttggtgttcaattttggcc-agtccttttggatttt-ctacatggtgaagctaaa----ctaatttatggttttttccacctttttt---ttttttttttgtacaaaagATATAGGTCTGACCGGGACAAAACTAGGATGTGGGGAAGGTGGTTGTGGAGCTTGCACAGTTATGGTTTCTCAATTTGATAGAAGATTGAAGAAATGCTC
| ||| | | | || ||| | | | | || | | || || | || | | | || |||||| | | | |||| |||| ||||||||||||| || ||||| || |||||||||||||| ||||||| || ||||| ||| | ||| || | |||| |||
gtgcttttaactctatattattgatttcttcaaatgcttatatctaatctaagtttagatagagtagagaagccacaaattgtacaatgcagcaaaatttagagggttaggttgttgtgtggtgggattcttgaaaacgttttttgtttcctttagATTTAGGATTGACCGGGACAAAGCTCGGATGCGGCGAAGGTGGTTGTGGGTCTTGCACCGTGATGGTGTCTAGTTATGACCGAGAGTCAAAGACATGTGT
upper sequence: GLYMA15G03870.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G34890.1 (Arabidopsis thaliana), 3'ss of exon 1
-ttggtg--ttcaattttggccagtcctt---ttggattttctacatggtgaagctaaactaatttatggttttttccaccttttttttttttttttgtacaaaagATATAGGTCTGACCGGGACAAAACTAGGATGTGGGGAAGGTGGTTGTGGAGCTTGCACAGTTATGGTTTCTCAATTTGATAGAAGATTGAAGAAATGCTC
||| | ||| || || || | ||| | | | |||||| | | || |||| | ||| | ||| || |||| |||| ||||||| ||||| || ||||| || |||||||||||||| |||||||| || ||||| ||| | ||| || | | |||| |
attgctagattcgcttggggacaaaaaatgacttgcagagatcaatctttttttctaaacgatcatgaagtagtttctaacttacagatgtttctt------gtagATTTAGGATTGACCGGTACAAAGCTGGGATGCGGCGAAGGTGGTTGTGGGGCTTGCACGGTGATGGTGTCTAGTTATGACAGGAAGTCAAAGACCTCTGT
upper sequence: GLYMA15G03870.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g02030.t01 (Vitis vinifera), 3'ss of exon 1
-ttggtgttcaattttggccagtccttttggattttctacatggtgaagctaaactaatttatggttttttccaccttttttttttttttttgtacaaaagATATAGGTCTGACCGGGACAAAACTAGGATGTGGGGAAGGTGGTTGTGGAGCTTGCACAGTTATGGTTTCTCAATTTGATAGAAGATTGAAGAAATGCTC
| ||| || | | | ||| | || || | | | | | | | | | | | | | ||| |||||| ||| ||||| ||||||||||| |||||||| | || ||||| |||||||||||||| |||||||| || ||||||||| | |||||| || | |||||||||
ctatttgtgtaactctttctagtgttgttttgttcttttagttcttatttttcttcatgtggtagcatctgat-tatcatttcccttttttggtaataaagACATAGGTCTGACGGGGACAAAGTTGGGCTGTGGCGAAGGTGGTTGTGGGGCTTGCACTGTGATGGTTTCTTATTTTGATGAAAATTCGAAGAAATGTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagctaaactaatttatggttttttccaccttttttttttttttttgtacaaaagATATAGGTCTGACCGGGACAAAACTAGGATGTGGGGAAGGTGGTTGTGGAGCTTGCACAGTTATGGTTTCTCAATTTGATAGAAGATTGAAGAAATGCTC
aactaat putative branch site (score: 2)
tttatggttttttcca CT-rich tract
ttttttccaccttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttggtgttcaattttggccagtccttttggattttctacatggtgaagctaaactaatttatggttttttccaccttttttttttttttttgtacaaaagATATAGGTCTGACCGGGACAAAACTAGGATGTGGGGAAGGTGGTTGTGGAGCTTGCACAGTTATGGTTTCTCAATTTGATAGAAGATTGAAGAAATGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
-tggtgtt
- - - - - - - - - - - ccttttg
- - - - - - - - - - - - - - - - - - - catggtg
- - - - - - - - - - - - - - - - - - - - - - - -gctaaac