Sequence
atgc intronic sequence ATGC exonic sequencegtgtcgctggcgcgctgtgtatgtgatttcatcttcttgcttgctttggatccattgtaatcttctttcttggctcttttgtgggacagTTGAGCGGCCATGGAAGACTAAAGACACAAGGCTTGTTCTTCAGGATGGATCAGTGTGGAATGGCAAGTCTTTTGGAGCTTCTGGAACGCAAGTCGGAGA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ07419 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ07419 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os02g47850.3 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------------------------------------gtgtcgctggcgcgctgtg--tatgtgatttcatcttcttgcttgctttggatccattgtaatctt--ctttcttggctcttttgtgggacagTTGAGCGGCCATGGAAGACTAAAGACACAAGGCTTGTTCTTCAGGATGGATCAGTGTGGAATGGCAAGTCTTTTGGAGCTTCTGGAACGCAAGTCGGAGA
|| ||| | || | || | ||| | | | | | | | || |||| | || ||| |||| | | ||||||||| | || | |||| |||||| ||||||| ||||| ||||| | |||||||||||| ||||| ||||| ||||| || ||
gtgagtcaggttgccttttcgctagctgattcgaatcgctctagttttgcagtcgcagcgcggaatacgtgctcagggttctgctacggatttgcgattaggcaattgtgctccacagttaagaagatgatgaatactgtttcaccatttttggattcttcgtg---cagTGCAAAGACCATGGAAGCTCAGCGATGCTCGGCTCGTTCTTGAGGATGGTTCAGTTTGGAAGGCCAAGTCTTTTGGTGCTTCAGGAACACAAGTTGGTGA
upper sequence: EFJ07419 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G029573_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------------------gtgtcgctggcgcgctgt-gtatgtgatttcatcttcttgctt---gctttggatccattgtaatcttctttcttggctcttttg------tgggacagTTGAGCGGCCATGGAAGACTAAAGACACAAGGCTTGTTCTTCAGGATGGATCAGTGTGGAATGGCAAGTCTTTTGGAGCTTCTGGAACGCAAGTCGGAGA
|| ||| ||| | | | ||| | | | | ||| | | | || | | | ||||| ||| || |||| |||||| | || | | ||||| || | |||||||||||||||| | |||||||||||| ||||| ||||| ||||| || ||
gtgggttgtctttactagctgttcagatatcaagttttgtattcggcagtcggcacgtggagtatgcgcttgggattttgtagcacgattcatcaattatgtaccttacaatttaagagctctattatttctggtttcactatttttgaaatctccatgcagCGGAAAGGCCGTGGAAGCTCAGTGATGCTCGTCTTGTCCTGGAAGATGGATCAGTGTGGACGGCCAAGTCTTTTGGTGCTTCAGGAACACAAGTTGGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgcttgctttggatccattgtaatcttctttcttggctcttttgtgggacagTTGAGCGGCCATGGAAGACTAAAGACACAAGGCTTGTTCTTCAGGATGGATCAGTGTGGAATGGCAAGTCTTTTGGAGCTTCTGGAACGCAAGTCGGAGA
tcttctttcttggctc CT-rich tract
attgtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtcgctggcgcgctgtgtatgtgatttcatcttcttgcttgctttggatccattgtaatcttctttcttggctcttttgtgggacagTTGAGCGGCCATGGAAGACTAAAGACACAAGGCTTGTTCTTCAGGATGGATCAGTGTGGAATGGCAAGTCTTTTGGAGCTTCTGGAACGCAAGTCGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT