Sequence
atgc intronic sequence ATGC exonic sequence...ggctattgtgcaaatgtgctaacagttgtttattactgcctcttacattgttgttaattttgtggtttgatttgcttactttgtccctttctgccttcagTGCTTGTGGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG
Basic information
species | Glycine max |
transcript | GLYMA02G06350.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G06350.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g12710.1 (Oryza sativa), 3'ss of exon 5
ggctattgtgcaaatgtgctaacagttgtttattactgcctcttacatt-gttgttaattttgtggtttgatttgcttactttgtccctt--tctgccttcagTGCTTGTGGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG
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agctctttt-cacttctgttaa--gttcactttaactccccgttttatcagccatgattgcagcagatcaattaatctgtagaaaactttatcttgtgcacagTTTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTGTGTGAGCTTGACATCGTATTTAACTTCAACAAG
upper sequence: GLYMA02G06350.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G177914_T05 (Zea mays), 3'ss of exon 4
ggctattgtgcaaatgtgctaacagttgtttat-tactgcctcttacattgttgttaattttgtggtttgatttgcttactttgtccctttct-gccttcagTGCTTGTGGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG-----------------------------
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-ataactgaagacttattttgtcttccttttgtctaaaaggacttat-cagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGGTACCATATGTCCATATGATCCTACTTTT
upper sequence: GLYMA02G06350.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G177914_T03 (Zea mays), 3'ss of exon 4
ggctattgtgcaaatgtgctaacagttgtttat-tactgcctcttacattgttgttaattttgtggtttgatttgcttactttgtccctttct-gccttcagTGCTTGTGGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG
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-ataactgaagacttattttgtcttccttttgtctaaaaggacttat-cagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG
upper sequence: GLYMA02G06350.2 (Glycine max), 3'ss of exon 5
lower sequence: AT3G50860.1 (Arabidopsis thaliana), 3'ss of exon 4
ggctattgtgcaaatgtgctaacagttgtttattactgcctcttacattgttgtt--aattttgtggtttgatttgcttactttgtccctttctgccttcagTGCTTGTGGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG
||||| | | | || || || || ||| | | ||| | | | | | || |||| | | || || |||| ||||| |||||| |||||||||||||||| ||||| || || || || || ||||||||||| || |||
-atcattgt-ctattcctctgctcgtaaattctttttgcttaacgctttgaaaatgtattctcattgtatgatgatttaaagttagtttcttgcattggcagTTCTTGTTGAAACACTGGACAAATGCTTCAGCAATGTCTGCGAACTCGACATTGTGTTCAACTACAGCAAG
upper sequence: GLYMA02G06350.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g01770.t01 (Vitis vinifera), 3'ss of exon 4
-ggctattgtgcaaatgtgctaacagttgtt-tattactgcctcttacattgttgttaattttgtggtttgatttgcttactttgtccctttctgccttcagTGCTTGTGGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG
| ||| | || | | || | || || | || || |||||||| || | | ||||| ||||| | | ||||||||||||| || ||||||||||||||||| ||||||| ||||||||| |||||||| || |||||||| ||||| |||
agcatatcatcttcatatcaaataagctaaaatacaacagtgcttttgatatttgttaat--ggtcatatcatttgtttactcttgactcttctgccttcagTTCTGGTGGAAACATTGGACAAGTGCTTCAAAAATGTATGCGAGCTTGACATAGTGTTCAATTATAGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattgttgttaattttgtggtttgatttgcttactttgtccctttctgccttcagTGCTTGTGGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG
tgcttac putative branch site (score: 2)
tttgcttactttgtcc CT-rich tract
ttgttaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggctattgtgcaaatgtgctaacagttgtttattactgcctcttacattgttgttaattttgtggtttgatttgcttactttgtccctttctgccttcagTGCTTGTGGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
-gctattg
- - - - - - - - tgctaac
- - - - - - - - - - - - - - - - - - tgcctct
- - - - - - - - - - - - - - - - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg