Sequence
atgc intronic sequence ATGC exonic sequencegttcctactttctttatgtttcttccaggcgagGATGGAACGGGGAAATCGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ23805 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os01g50360.1 (Oryza sativa), 3'ss of exon 2
----------------------------------------------------------------------------gttcctactttctttatgtt-----tcttccaggcgagGATGGAACGGGGAAATCGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGA
||| | | | || || | | || | | || || | || ||||| ||| ||||||||||||||||||| ||||| ||| ||||||||| ||||| ||||| || ||
gtttggatttcgttaacggttttaccttcggttcttgtagcaattactaatagctagatttatagcctgatttgccgtttttgatgaccttgaattgaagGTGAGCACGGTGCAGTTGTAAACAAGGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG--------------
upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os03g02960.1 (Oryza sativa), 3'ss of exon 1
----------------------------------------------------------------------------gttcctactttctttatgtt-----tcttccaggcgagGATGGAACGGGGAAATCGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGA
||| | | | || || | | ||| | |||| | | || ||||| ||| ||||||||||||||||||| ||||| ||| ||||||||| ||||| ||||| || ||
aatggtgtctctttcggttcttgtagcaattactaatgtactactctagatagcaagatttatagcctgacttgcagttttaaatgaccttgaattgaagGTGAACAAGGTGCAATCGGAAACGAGGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG--------------
upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os07g22450.1 (Oryza sativa), 3'ss of exon 1
----------------------------------------------------------------------gttcctactttctttatgttt--cttccaggcgagGATGGAACGG--GGAAAT-------CGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGA
|| | ||| | || || ||| ||| | || | | | |||| | ||||| ||| ||||||||||||||||||| ||||| ||| ||||||||| ||||| ||||| || ||
tgtttggatttcgttaacggtgttaccttcagttcttgtagcaattactaatagctagatttatagcctgatttgcagttttgatgaccttgaattgaagGTGAGCACGGTGCAGTTGTAAATAAAGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG--------------
upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G171466_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------------------------------------gttcctactttctttatgtttcttccaggcgagGATGGAACGGGGAAATCGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGA
| | | | | | ||||| | | ||| | | | ||||| ||||||||||||||||||||||| ||||| ||| ||||||||| ||||| ||||| || || || || ||
gtaacgacgacgtgtgtgttatctgttcccttctgcgttcagcacgcagacagatttaatttgcacgtgccagacgtggactgatttgagctgcggtgtctcgctctgggcgtgtagGCGCCGGCGCAACCGAGGGCACCAAGCAGAGCCGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACCGGCGTCACCAG-----
upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G000923_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------------gttcctactttctttatgtttctt--ccaggcgagGATGGAACGGGGAAATCGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGA
|| | | || || |||| | || | ||||| | || || || ||||||||| |||| |||||||||||||| ||||| |||| |||||| || ||||||||| | ||||| || | |
tcctgtgcgctttgaatttgctgtctgtttttatctctggtatgtgaaacaattacaacacctgacaagtatttgtctcattttcatctttcgcgacaagAAGGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCG-----
upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G000923_T02 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------gttcctactttctttatgtttctt--ccaggcgagGATGGAACGGGGAAATCGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGA
|| | | || || |||| | || | ||||| | || || || ||||||||| |||| |||||||||||||| ||||| |||| |||||| || ||||||||| | ||||| || | | ||
tgtgcgctttgaatttgctgtctgtttttatctctggtatgtgaaacaattacaacacctgacaagtatttgtctcattttcatctttcgcgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT--
upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G465333_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------------------------gttcctactttctttatgtttcttccaggc-gagGATGGAACGGGGAAATCGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGA
|| | | || || || || | | ||||| | || || || ||||||||| |||| |||||||||||||| || || |||| |||||| || ||||||||| | ||||| ||
taacctgcaccctttgaatttgctgtctgtttttatctctggtgtgtgaaacaattgcagacctgtatctgacaagtattggtgtcattttcatcttcagGACAAGAAGGGGATGCCAGCGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAAGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGT-----------
upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv16s0098g00830.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------------------------gttcct-actttctttatgtttctt--ccaggcgagGATGGAACGGGGAAATCGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGA-
|| | | | ||| | | ||| ||| | | || || | | || ||||| ||| | || |||||||||||||| ||||||||| ||||||||| ||||| ||||| ||||| || ||||| |
ctgtatccaattatctaattcttgtttacatactctttttaatattcaattacaatgaagattgtccttgaatttatctcagttgggaaatgaggtgcagGTGCAAATGAGGGCTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCAC
upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: EDO97954 (Chlamydomonas reinhardtii), 3'ss of exon 1
------------------------------------------------------------------------gttcctactttctttatgtttcttccaggcgagGA---TGGAACGGGGAAATCGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGA
| | | | ||||| | ||| ||||| ||| | || ||||| ||||| ||||||||||||||||| ||||| ||||||||||| || ||||||||||| ||||| || ||
gctcagcgtctggcgctgtcggctgggcgagcgatgccagctttagtttcgtcggcccacagggatgctgaacatggcgcatgtgtgatgttggctgcagATGAGGAGGGTGGCGCTGGCCGCGGCAAGCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGAC--------
upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S539_1V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------------------------------------------gttcctac-tttctttatgtttcttccaggcgagGATGGAACGG---------GGAAATCGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGA
||| ||| ||||| | |||| || |||| | | | || || ||||| ||||| | |||||||||||| ||||||| ||||| ||||| || ||||||||||||||||
gtcctttccatcaaatccccttcccatacttttcgtaactcttgcctttgttgacaagactgtgagtaattcttagttagacatctcgtctttcttgatagggaatttcacgtgtttacatatgtacttcgcagGTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACTGA--------------
upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------------------------------------------------gttcctactttctttatgtttcttccaggcgagGATGGAACGGG---------GAAATCGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGA
||| ||| || | | |||||| |||| || ||||| | || || || ||||| ||||| | |||||||| ||| ||||||| ||||| ||||| || |||||||||||||| |
gtctgttgtcaacgacccttgccaacgtctattgacccaagcctctgttcagaattagtgagtgatgctttctaaaattgtaagctagaggcattactctgtttgatcgagtttctaaattttct---tttcttgcagGTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGAAGAAAAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACCGA-------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttcctactttctttatgtttcttccaggcgagGATGGAACGGGGAAATCGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGA
ttcctactttctttat CT-rich tract
tttctttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcctactttctttatgtttcttccaggcgagGATGGAACGGGGAAATCGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC