Sequence
atgc intronic sequence ATGC exonic sequencegttttccttcgagttataactagtttcctatccagATGGACTACATTCTCGGGAAGAACCCACGGCATATGAGCTACGTTGTGGGATTCGGCAACAAGTATCCCAAGTACGTCCACCACCGAGCAGCATCGGTTC
Basic information
species | Selaginella moellendorffii |
transcript | EFJ31524 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ31524 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os03g52630.2 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------gttttccttcgagttataactagtttcctatccagATGGACTACATTCTCGGGAAGAACCCACGGCATATGAGCTACGTTGTGGGATTCGGCAACAAGTATCCCAAGTACGTCCACCACCGAGCAGCATCGGTTC
| | || || || | | ||| | || || | || || |||||||||| | | ||||||||||||||||| || || |||||||| |||||| || || ||| ||| ||||| | |
gtaaggttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGTTTTGGAAACAAGTACCCCAAGCGCGCTCATCACAGAGGTGCATCAATCC
upper sequence: EFJ31524 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G110735_T01 (Zea mays), 3'ss of exon 5
-----------------------------------------------------gttttccttcgagttataactagtttcctatccagATGGACTACATTCTCGGGAAGAACCCACGGCATATGAGCTACGTTGTGGGATTCGGCAACAAGTATCCCAAGTACGTCCACCACCGAGCAGCATCGGTTC
|| | | ||| | || ||| | | ||| | |||||||| || || ||||||||| | | ||||||||||||||||| ||||| |||||||| || ||| | || ||| ||| || ||| | |
gtaaaagcattgttcttaatgctctcaaagtgcccaacgtacggggaagtgaaattgatagttaaattaaatct-gttaaatttgcagCTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCATCACAGAGGCGCGTCGATAC
upper sequence: EFJ31524 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G147849_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------------gttttccttcgagttataactagtttcctatccagATGGACTACATTCTCGGGAAGAACCCACGGCATATGAGCTACGTTGTGGGATTCGGCAACAAGTATCCCAAGTACGTCCACCACCGAGCAGCATCGGTTC
| ||||| || | | | | ||| | |||||||| || || ||||||||| | | ||||||||||||||||| ||||| |||||||| || ||| | |||||| ||| || ||| | |
gtaaatcgttcttcttaactctccttaggtgcccaaccttacattagcagagaaagtgggtcggtagttaaaatctgctcgatttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCACCACAGAGGTGCGTCGATAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttccttcgagttataactagtttcctatccagATGGACTACATTCTCGGGAAGAACCCACGGCATATGAGCTACGTTGTGGGATTCGGCAACAAGTATCCCAAGTACGTCCACCACCGAGCAGCATCGGTTC
ttataac putative branch site (score: 2)
tttcctatcc putative PPT
ttataacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttccttcgagttataactagtttcctatccagATGGACTACATTCTCGGGAAGAACCCACGGCATATGAGCTACGTTGTGGGATTCGGCAACAAGTATCCCAAGTACGTCCACCACCGAGCAGCATCGGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG