Sequence
atgc intronic sequence ATGC exonic sequencegtacgtattacacttaagttcttctttgccgttgtcctctttggaactctaaagaatctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ24245 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 2
---------------------gtacgtattacac-ttaagttcttctttgccgttgtcc---tctttggaactctaaagaatc-tatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
| || ||| | ||| | | ||| || | | ||| || | | | | || | || ||||| | || ||||| || | ||||||||| | || |||||||||||||||||||||| ||| |||||| | ||||| || |||
atatttctagcaactctgataatttttactactcgctaattacgagtttattattttgtgaattattgcctaattacatacttatttctttttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG
upper sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os01g36950.3 (Oryza sativa), 3'ss of exon 2
---------------------gtacgtattacac-ttaagttcttctttgccgttgtcc---tctttggaactctaaagaatc-tatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG----------------
| || ||| | ||| | | ||| || | | ||| || | | | | || | || ||||| | || ||||| || | ||||||||| | || |||||||||||||||||||||| ||| |||||| | ||||| || |||
atatttctagcaactctgataatttttactactcgctaattacgagtttattattttgtgaattattgcctaattacatacttatttctttttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAGGTACCATTGATCTTCA
upper sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM5G860590_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------------------------------gtacgtattacacttaagttcttctttgccgttgtcctctttggaactctaaagaa--------------tctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
| | || ||| || | ||| ||| | | || || | ||||| | || ||||| |||| || ||||| |||||||||||| || | || ||||||||||||||||||| ||| ||||| | ||||| ||||||
gtgaggtccaaactatacctactctactctactcttttgtgtttatcatcatcatcattattactcgatcagtcgtatgcatatgattccatcatttcagcatctttatctttcaatcatgcttgtggttactaaatataaaaaaagaagggggaaatttctcatcgtctatgggacgaacgcagGCTGCAAGCTTCGGAGGATCCAACATCGATCCAGCAGCTTGGGAGGACAAGAAGTGCCCCGGCGAGTCCCGCTTCCCTGCTCAG
upper sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM5G860590_T02 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------------------gtacgtattacacttaagttcttctttgccgttgtcctctttggaactctaaagaa--------------tctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
| | || ||| || | ||| ||| | | || || | ||||| | || ||||| |||| || ||||| |||||||||||| || | || ||||||||||||||||||| ||| ||||| | ||||| ||||||
gtccaaactatacctactctactctactcttttgtgtttatcatcatcatcattattactcgatcagtcgtatgcatatgattccatcatttcagcatctttatctttcaatcatgcttgtggttactaaatataaaaaaagaagggggaaatttctcatcgtctatgggacgaacgcagGCTGCAAGCTTCGGAGGATCCAACATCGATCCAGCAGCTTGGGAGGACAAGAAGTGCCCCGGCGAGTCCCGCTTCCCTGCTCAG
upper sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AC207342.3_FGT008 (Zea mays), 3'ss of exon 2
--------------------gtacgta--ttacacttaagtt-cttctttgccgttgtcctctttggaactctaaagaatctatcaatccaatc--cagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
||| | | | | | || | | || | | || | | |||| | | ||| ||| ||| ||||| | || || || || |||||||||| | || |||||||||||||||||||||| ||| |||||| | ||||| || |||
gtacggtacagtacattacagtagccagccaattcctgatttgccttttcatcttcatctgcatctatgctctcatggatccggt--tccgatcaccagGCCGCCAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG
upper sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G071154_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------gtacgtattacacttaagttcttctttgc-cgttgtcctctttggaactctaaagaatctatcaatccaat--ccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
| ||| |||||||| | || ||| || | || | | || ||| || |||||| | || || || || |||||||||| | || |||||||||||||||||||||| ||| |||||| | || || || |||
gtacagtacagcacagcacagcacagtagccactagccagttcgtggttccctttccttgcttcttcttcgttcgctgtccttgc-ttcttcttcgttcgctgtattcacgaggaccc----ggttccgatcctccgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG
upper sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA20G16100.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------------------------------------------gtacgtattacacttaagttcttctttgccgttgtcctctttggaact--ctaaagaatctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
| | |||| ||| || | || | | | | |||| | | | ||||| ||||||||||||| ||||| || ||| |||| || ||||||||||||||||||| || || || | ||||| ||||||
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG
upper sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA20G16100.3 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------------------------------------------gtacgtattacacttaagttcttctttgccgttgtcctctttggaact--ctaaagaatctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG----------------
| | |||| ||| || | || | | | | |||| | | | ||||| ||||||||||||| ||||| || ||| |||| || ||||||||||||||||||| || || || | ||||| ||||||
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGGTATATATCATCTCAT
upper sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv02s0025g01720.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------------------------gtacgtattacacttaa-gttcttc-tttgccgttgtcctctttggaactctaaagaatctatcaatccaat--ccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
| ||||| | | || ||| | || ||| | | || | | || ||| | | | || ||||| |||| |||||||| | ||||| ||| ||||||| ||||||||||||||||||| || || || | ||||| ||||||
gtttgtatttctttctaagaatcataaactctgcagtaattcatgtattcttttggggttttctcaaaaatattagattcaatattcagcacttcatgttttggattatgcaccattacctaatgttatacttgtatgttcagGCTGCAAGCTTTGGAGGAACAAACATTGATCCAACTGCTTGGGAGGACAAGAAGTGCCCTGGCGAATCACGCTTCCCTGCTCAG
upper sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S6_446V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------gtacgtattacacttaagttcttctttgccgttgtcctctttggaactctaa-agaatct-------atcaat-ccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
||| || || || ||| | | || || | | | | ||||| | || | | |||| |||| ||||||||||||||||| ||| |||| || ||||| |||||||||||||||||||| || ||||| || || |||
tgatacatgacagagcagtagttaccgcatttgctacgcgcttcgaatgtaaagaagatgaaattatgatacaatctcatgagaaacagtgtctgattagGCTGCAAGCTTTGGAGGCTCCAACATAGATCCAACAGCTTGGGAAGACAAGAAGTGCCGCGGAGAATCAAGATTTCCTGCACAG
upper sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S4_323V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------gtacgtatt---acacttaagttcttctttgccgttgtcct---ctttggaactc-taaagaatctatcaatccaatc---cagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
| |||| | || | || | | ||| | | || ||| | | | | | || | | |||||| |||||||||||||||| ||||| ||| |||| || ||||| |||||||| || || |||||||| ||||| || || |||
caaggaggacctacttggacgtcctctgacctgtgggtggtgtcaaggacttgcttcagacgtaggttctcatgtatggtgtttacattctgtatgacagGCAGCAAGTTTTGGAGGCTCTAACATAGATCCAACCGCCTGGGAAGACAAGAAATGTCGGGGAGAGTCAAGATTTCCTGCCCAG
upper sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S168_104V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------gtacgtattacact-taagttcttctttgccgttgtcctctttggaactctaaagaat-ctatcaatc--caatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
| | | | | || | | | | | || | | || |||| | || ||| || | |||||| |||||||||||||||| ||||| || |||| || ||||| |||||||| || || ||||| |||||||| || ||||||
gagaagcaaggaagatcaatttcaacatctgtgaggttgtaggatgtattatattctt--ctggtatgaggtgctaatgcatgtcgtcattctttatgacagGCAGCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG
upper sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 3
--------------------gtacgtattacact-taagttcttctttgccgttgtcctctttggaactctaaagaatct-atcaatcc--aatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
| | | | | || | | | | | || | | || |||| | || | ||| || | |||||| |||||||||||||||| ||||| || |||| || ||||| |||||||| || || ||||| |||||||| || ||||||
agcaaggaagatcaatttcaacatctgtgaggttgtaggatgtattatattctt--ctggtatgaggtgctaatgcatgtcgtcattctttatgacaggcagCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttctttgccgttgtcctctttggaactctaaagaatctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
ctctaaa putative branch site (score: 3)
taaagaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtattacacttaagttcttctttgccgttgtcctctttggaactctaaagaatctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA