Sequence
atgc intronic sequence ATGC exonic sequence...ttggatctgatgacttctattaatggtttttgataatatatcaatattctgatttgtacatactcaattcacttattcccatttttattttgttctacagCCTTGTTCAATGGGCTTTGCCACTGGTGGACAAACATTCTTTTTGTGGGGAGGGTGCATGATGGCAA
Basic information
species | Glycine max |
transcript | GLYMA16G08510.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g67870.1 (Oryza sativa), 3'ss of exon 7
ttggatctgatgacttctattaatggtttttgataatatatcaatattctgatttgtacatactcaattcacttattcccattt-ttatt-----ttgttctacagCCTTGTTCAATGGGCTTTGCCACTGGTGGACAAACATTCTTTTTGTGGGGAGGGTGCATGATGGCAA
||| | | | || | ||| ||| || |||| | |||| || | || ||| || | |||| || | | | |||||||||||||| || ||||| |||||||| | || |||||||||||||| || |||||||||
------ctgttttcgtaagctagttatttagttctgtatctccctatttttatttttatttttattttttactcttttcgatttactaataaagaccatattgcagCCTTGTTCAATTGGATTTGCAACTGGTGGGAAGACTTTCTTTTTGTGGGGTGGCTGCATGATG----
upper sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 7
ttggatctgatgacttctattaatggtttttgataatatatcaatattctgatt-tgtacatactcaat--tcacttattcccatttttattttgttc----tacagCCTTGTTCAATGGGCTTTGCCACTGGTGGACAAACATTCTTTTTGTGGGGAGGGTGCATGATGGCAA
| | | | || | ||||| | || | | || || || | || || | | || | || ||| ||||| | |||||||| |||||||| ||||| ||||||||| ||||||||||||||||||||| || ||||||
----gtacggtagatataatcactggttacttttatcaagttgttaggttgtttataattgtagcatatcgtaatttgagctaatatttggcatgttcactttccagCCTTGCTCAATGGGATTTGCGACTGGTGGAAGAACATTCTTTTTGTGGGGAGGATGTATGATG----
upper sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv11s0016g03130.t01 (Vitis vinifera), 3'ss of exon 7
ttggat-ctgatgacttctattaatggtttttgata-atatatcaatattctgatttgtacatactcaattcacttattcccatttttattttgttctacagCCTTGTTCAATGGGCTTTGCCACTGGTGGACAAACATTCTTTTTGTGGGGAGGGTGCATGATGGCAA
| || || ||| | | | | ||| || || || | | | || | | || || | ||| | || | ||||||||||||| ||||| || || || |||||| ||||||||||||||||||||||||| ||||||
gtacatattggtgatagatccttcaactcctgaatagattgatttgtacttattagagaaaatgtctagattgattttttttgtcttt--tctgatttacagCCTTGTTCGATGGGTTTCGCTACAGGTGGAAAAACATTCTTTTTGTGGGGAGGGTGTATGATG----
upper sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ38341 (Selaginella moellendorffii), 3'ss of exon 6
ttggatctgatgacttctattaatggtttttgataatatatcaatattctgatttgtacatactcaattcacttattcccatttttattttgttctacagCCTTGTTCAATGGGCTTTGCCACTGGTGGACAAACATTCTTTTTGTGGGGAGGGTGCATGATGGCAA
| || || | | | | || | | | | | | | | ||||| |||||||| || ||||| || |||||| ||| |||||||||||||| || |||||||||
---------------------------------------------gtaaagactt-tgaaaattttgctctccagatactgatatcaagacgattatcagCCCTGTTCAATTGGTTTTGCGACCGGTGGAAGAACTTTCTTTTTGTGGGGCGGATGCATGATG---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctgatttgtacatactcaattcacttattcccatttttattttgttctacagCCTTGTTCAATGGGCTTTGCCACTGGTGGACAAACATTCTTTTTGTGGGGAGGGTGCATGATGGCAA
ttctgat putative branch site (score: 3)
ttcccatttttatttt putative PPT
atttttattttgttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttggatctgatgacttctattaatggtttttgataatatatcaatattctgatttgtacatactcaattcacttattcccatttttattttgttctacagCCTTGTTCAATGGGCTTTGCCACTGGTGGACAAACATTCTTTTTGTGGGGAGGGTGCATGATGGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - -tgatgac
- - - - - - - - - - - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - catactc