Sequence
atgc intronic sequence ATGC exonic sequencegtatggatagccacacgatcgatccattgaattctctgatctttcttctccctctcatagAAATGCCTGGATGCTCGATCCAATCCCTCGCCCCCCTGCGCGACGGTGCCCAAGAAGGACTACATCAAGCCGCTCGTCTTCCACGACGGCCGCCTCATCA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ35133 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ35133 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os01g14900.1 (Oryza sativa), 3'ss of exon 1
-----------------------------------------gtatggatagccacacgatcgat--ccattgaattctctg-atctttcttctccctctcatagAAATGCCTGGATGCTCGATCCAAT------CCCTCGCCCCCCTGCGCGACGGTGCCCAAGAAGGACTACATCAAGCCGCTCGTCTTCCACGACGGCCGCCTCATCA
| || | |||| || || | ||| | | || || | || ||| | | | | | | || | | | | || || || ||| | || | | | |||||||||||||||||||||||||||
atcaactactgttacttagttaacaccgttgttatcacagagcgtg-acgtgtacacaattaatgtcaattaattaacgtgcatgtgtccaatccttgcagGAAACCTTCACTGCGACTGAGGCTGACAAGCGGCGGTGGCGGCCGCTGCCGCCGGGCGGCGAGTGCGGCGGCGTCAAGCCGCTCGTCTTCCACGACGGCC---------
upper sequence: EFJ35133 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os01g44069.1 (Oryza sativa), 3'ss of exon 1
-------------------------------gtatggatagccacacgatcgatccattgaattctctgatctttcttctccctctcatagA--AATGCCTGGATGCTCGATCC--AATCCCTCGCCCCCCTG---CGCGACGGTGCCCAAGAAGGACTACATCAAGCCGCTCGTCTTCCACGACGGCCGCCTCATCA---
| ||||| | | | || | | | | | | || | | | | || || | ||| | | | || || | | || |||| | |||| | | ||| ||||||||| |||||||||||||||||||| |
aaaaattccacagctgtatttaaattgggacggatggaatactatagtcgtagtctagt-agtacacagagtacttaccacagttggattgattactgcagGAAGTTTACGTCGTGAACAGGGAGAGCACCAAGACCGCGCGGCTGCCGCGGGACAGGTACCCGAAGCCGCTCATCTTCCACGACGGCCGCCTCGCCTTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatagccacacgatcgatccattgaattctctgatctttcttctccctctcatagAAATGCCTGGATGCTCGATCCAATCCCTCGCCCCCCTGCGCGACGGTGCCCAAGAAGGACTACATCAAGCCGCTCGTCTTCCACGACGGCCGCCTCATCA
ctctgat putative branch site (score: 4)
ttctctgatctttctt CT-rich tract
attgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggatagccacacgatcgatccattgaattctctgatctttcttctccctctcatagAAATGCCTGGATGCTCGATCCAATCCCTCGCCCCCCTGCGCGACGGTGCCCAAGAAGGACTACATCAAGCCGCTCGTCTTCCACGACGGCCGCCTCATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG