Sequence
atgc intronic sequence ATGC exonic sequencegtgagttggttctgggactccgattccgaagtgaatctcacgtttggttacttcttttgggtacagACTGTTGACAAGTTGATCGAAACTGGAGACAGTGAGACAATTTTTCAAAAGGCTGTTCAGGAACAAGGCCGAGGCCAA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ08209 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ08209 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: LOC_Os06g07200.1 (Oryza sativa), 3'ss of exon 9
-------gtgagttggttctgggactccgattccgaagt--gaatctcacgt-ttggttacttcttttggg---tacagACTGTTGACAAGTTGATCGAAACTGGAGACAGTGAGACAATTTTTCAAAAGGCTGTTCAGGAACAAGGCCGAGGCCAA
|| || | | | || || | | || | || ||| |||| || | ||||| |||||||| |||| |||||||| ||||||||| ||||||||| | ||| |||||||||||||||| ||
gtaagaagtatattaacttcaaatcatctgttaacaaatctgcatatggtgtgttgcttacacctggccaaattttcagACAATTGACAAGCTGATAGAAACTGGGGACAGTGAGCAAATTTTTCAGAGAGCTATTCAGGAACAAGGCCGTGGAAGG
upper sequence: EFJ08209 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA16G27050.1 (Glycine max), 3'ss of exon 9
----------------------------gtgagttggttctgggactccgat----tccgaagtgaatctcacgtttggttacttcttttgggtacagACTGTTGACAAGTTGATCGAAACTGGAGACAGTGAGACAATTTTTCAAAAGGCTGTTCAGGAACAAGGCCGAGGCCAA
| || || | | | | | || || | | | | | | | | | |||||||| |||||| || || ||||||||||| ||||| |||||| || |||||| ||||||||||||| ||||||||
gtattctttcttttcttaactattattcattagctgatgcagagctgatggaaatgtcttttaggagtttgtcttctaatcatataact-atgtacagACAATTGACAGATTAATTGAAACTGGAGATAGTGAACAAATTTTCCAGAAGGCTATTCAGGAACAAGGACGAGGCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgggactccgattccgaagtgaatctcacgtttggttacttcttttgggtacagACTGTTGACAAGTTGATCGAAACTGGAGACAGTGAGACAATTTTTCAAAAGGCTGTTCAGGAACAAGGCCGAGGCCAA
atctcac putative branch site (score: 3)
ttacttctttt putative PPT
ttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttggttctgggactccgattccgaagtgaatctcacgtttggttacttcttttgggtacagACTGTTGACAAGTTGATCGAAACTGGAGACAGTGAGACAATTTTTCAAAAGGCTGTTCAGGAACAAGGCCGAGGCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT