Sequence
atgc intronic sequence ATGC exonic sequencegtaaagtttcgattgctttcagtcataaggaaaatgttctaactatcaacacttcgcagCAGATCAGCTTCCAGGAGTTCAAAAACAAGCTTCTGGAGACTGGTCTCGTTGATCACATAGAGGTTGTGAATAAGGCGGTCGCAAGAGTATATGTTCGCG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ31204 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ17143 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA11G14640.1 (Glycine max), 3'ss of exon 1
-----------------------------------gtaaagtttcgattgcttt-cagtcataaggaaaatgttctaactatcaa--cacttcgcagCAGATCAGCTTCCAGGAGTTCAAAAACAAGCTTCTGGAGACTGGTCTCGTTGATCACATAGAGGTTGTGAATAAGGCGGTCGCAAGAGTATATGTTCGCG---
|| ||||| || || || || | || | | || ||| |||||||||||| |||||||| |||||||||||| |||| | || | || || || || | || |||| | || || | ||||||||| |
accagcaaggtacctgttcgtctgtgtctggttttatatggtttcttttatttcattgttatcatctttctgacgtggatcagaatttgattctttgcagATCAGCTTTCAGGAGTTTAAAAACAAGCTTTTGGAACCAGGATTAGTAGACCATATTGTTGTCTCAGATAAATCAGTTGCCAAAGTATATGTAAGGAACA
upper sequence: EFJ17143 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT1G07510.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------------------gtaaagtttcgattgctttcagtcataaggaaaatgttctaactatcaacact-------tcgcagCAGATCAGCTTCCAGGAGTTCAAAAACAAGCTTCTGGAGACTGGTCTCGTTGATCACATAGAGGTTGTGAATAAGGCGGTCGCAAGAGTATATGTTCGCG---
|| | | | | | | | | ||||| | |||| |||| | | | ||||| || ||||||||||||||||||||||| || ||| ||||| | || ||||||||||| ||| ||||| | ||||||| ||| ||||| |
gcaagcatgtccaactatactctgtgtatcatgttatctatataactgcagacgtgt--gggcctgaggaatgtcaactaattatccgtgttatatttgttggttcagATTAGTTTCCAGGAGTTCAAAAACAAGCTCCTCGAGGCTGGTTTAGTGGATCACATAGATGTTTCCAATAAAGAAGTCGCAAAAGTCTATGTGAGGAGTT
upper sequence: EFJ17143 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------------------gtaaagtttcgattgc--tttcagtcataagga------aaatgttctaactatcaacacttcgcagCAGATCAGCTTCCAGGAGTTCAAAAACAAGCTTCTGGAGACTGGTCTCGTTGATCACATAGAGGTTGTGAATAAGGCGGTCGCAAGAGTATATGTTCGCG---
| | | | || || || || | ||| | ||| | | | ||||| || ||||||||||||||||||||||| || ||| ||||| | ||||| |||||||| ||| || || | || |||| ||| || || |
gcaagcatatttaaactaagctttgtgatattcttggatatggaactgcagatgtggttctgctcgtatagtttccactaatatcctatgctaccttttattgtttcagATAAGTTTCCAGGAGTTCAAAAACAAGCTACTCGAGCCTGGTTTAGTTGACCACATAGATGTTTCAAACAAATCAGTAGCAAAAGTCTACGTGAGGAGCA
upper sequence: EFJ17143 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S39_149V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------gta-aagtttcgattgctttcag--tcataaggaaaatgttctaactatcaacac----ttcgcagCAGATCAGCTTCCAGGAGTTCAAAAACAAGCTTCTGGAGACTGGTCTCGTTGATCACATAGAGGTTGTGAATAAGGCGGTCGCAAGAGTATATGTTCGCG---
||| | | | | | ||| || | ||| || || | | || | ||| ||||||||||||||||||| || || |||||||| |||||| | ||| | || ||| || || || || ||| | || | ||| ||||||
gtttcttttctccatgtatgtatgtatgcatgtatgtgatccactgggtttgaggttgatagttaatttgattcttttttcgtgataatattcaaagcagATCAGCTTCCAGGAATTTAAGAACAAGCTGCTGGAGCCGGGTATGGTAGATAGAATTGAAGTCACTAACAAGAGCTTTGCGAAAGTTTATGTTAAAACAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|70670730|gb|DN839307.1|DN839307EST: TTGCGATTCTTCTCAGCTCATTATCTGTGAGGTTCAACGGTACGCGCCAG -A--TCAGCTTCCAGGAGTTCAAAAACAAGCTTCTGGAGACTGGTCTCGTT
genomic: TTGCGATTCTTCTCAGCTCATTATCTGTGAGGTTCAACGGTACGCGCCAGgtaaagtttc ... cacttcgcagCAGATCAGCTTCCAGGAGTTCAAAAACAAGCTTCTGGAGACTGGTCTCGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtttcgattgctttcagtcataaggaaaatgttctaactatcaacacttcgcagCAGATCAGCTTCCAGGAGTTCAAAAACAAGCTTCTGGAGACTGGTCTCGTTGATCACATAGAGGTTGTGAATAAGGCGGTCGCAAGAGTATATGTTCGCG
ttctaac putative branch site (score: 1)
aaaatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagtttcgattgctttcagtcataaggaaaatgttctaactatcaacacttcgcagCAGATCAGCTTCCAGGAGTTCAAAAACAAGCTTCTGGAGACTGGTCTCGTTGATCACATAGAGGTTGTGAATAAGGCGGTCGCAAGAGTATATGTTCGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA