Sequence
atgc intronic sequence ATGC exonic sequencegtaagccccctttttcccccaaatccagtctctcggacatgtatcgatgaaatcgctgacttgggcgattctctctctcccagAGGTGTGGCCGGCTGGACGATCAGATCGCTCTCCTCAAGCACAAGCTCCAGCTGATCTACGCGGGCCTCGCCTTCAATGGCAAGCGGACCAAGACCGCGC
Basic information
species | Selaginella moellendorffii |
transcript | EFJ30150 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ30150 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os09g36740.1 (Oryza sativa), 3'ss of exon 2
-gtaagccccctttttcccccaaatccagtctctcggacatgtatcgatgaaatcgctgacttgggcgattctctctctcccagAGGTGTGGCCGGCTGGACGATCAGATCGCTCTCCTCAAGCACAAGCTCCAGCTGATCTACGCGGGCCTCGCCTTCAATGGCAAGCGGACCAAGACCGCGC
| | |||| | |||||| | | ||| | | || | ||||| | | | ||| | |||| || || ||||||||||| |||||| | || |||||||||||||| ||||| ||| || ||||| ||||||||| |||||||| |||||||| ||||
gttcaatccccctcttccccttctcgccattgctctgcaacaatgcgcgcagcaagctgatgcgtgtcgatgaatctgagc-agAGATGCGGGCGGCTGGACGACCAGATCTCGCTGCTCAAGCACAAGCTGCAGCTCATCCACCAGGGCCACGCCTTCAACGGCAAGCGCACCAAGACGGCGC
upper sequence: EFJ30150 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G000825_T01 (Zea mays), 3'ss of exon 2
gtaagccccctttttcccccaaatccagtctctcgg-acatgta-tcgatg-aaatcgctgactt--gggcgattctctctct-----cccagAGGTGTGGCCGGCTGGACGATCAGATCGCTCTCCTCAAGCACAAGCTCCAGCTGATCTACGCGGGCCTCGCCTTCAATGGCAAGCGGACCAAGACCGCGC
|| | | | | | | | | | | |||| | || || ||||| | | ||| || | || | | | | | ||||| || || ||||||||||| || ||| | || |||||||||||||| ||||||||| || ||||| ||||||||| |||||||||||||| || || |
gttcgtgctcgtacttcgtctaccttaatttctctgcacgtgcgctcgattcatgcctctggctctgagacggtattaaatttaaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAGCTGATCAACCAGGGCCACGCCTTCAACGGCAAGCGGACCAAAACGGCTC
upper sequence: EFJ30150 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G050268_T01 (Zea mays), 3'ss of exon 2
--------------------------gtaagccccctttttcccccaaatcca-gtctctcggacatgtatcgatgaaatcgctgacttgggcgattctctctctcccagAGGTGTGGCCGGCTGGACGATCAGATCGCTCTCCTCAAGCACAAGCTCCAGCTGATCTACGCGGGCCTCGCCTTCAATGGCAAGCGGACCAAGACCGCGC
| || | | | | || || | |||| ||| | || || || |||| | | | | ||||| || || ||||||||||| || ||| | || |||||||||||| | |||| |||| || ||||| |||||||||||||||||||||||| || || |
gttcgtgctcgtccttcgtctaccttttgtgcacgtatgtgtgttaacattcatgcctctgagacggtattaaatttaaatgcgctcttgc-tgctgtcttgatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGTTGCAGCGGATCCACCAGGGCCACGCCTTCAATGGCAAGCGGACCAAAACGGCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctcggacatgtatcgatgaaatcgctgacttgggcgattctctctctcccagAGGTGTGGCCGGCTGGACGATCAGATCGCTCTCCTCAAGCACAAGCTCCAGCTGATCTACGCGGGCCTCGCCTTCAATGGCAAGCGGACCAAGACCGCGC
cgctgac putative branch site (score: 3)
cgattctctctctccc putative PPT
atgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagccccctttttcccccaaatccagtctctcggacatgtatcgatgaaatcgctgacttgggcgattctctctctcccagAGGTGTGGCCGGCTGGACGATCAGATCGCTCTCCTCAAGCACAAGCTCCAGCTGATCTACGCGGGCCTCGCCTTCAATGGCAAGCGGACCAAGACCGCGC
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