Sequence
atgc intronic sequence ATGC exonic sequencegtacttgatcggttctggaatggtaaagagccagagtttcttctttctcaggaactccaaagttcgcgtttccatccttgcaggatcctcagaccgagaacaatccatatctcgggttcgtctacacgtccttccagGAGCGAGCCACCACCATCTCTCACGGCAACACTGCTCGCCACGCCAAGGAGCACGGAGACCACAAGCTCGCGTGTTTGCGGCCTCATCGCAGCCGACGAG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ28408 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ28408 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os02g30200.1 (Oryza sativa), 3'ss of exon 3
gtacttgatcggttctggaatggt-------aaagagccagagtttcttctttctcaggaactccaaa--gttcgc---gtttccatc----cttgca-ggatcctcagaccgagaacaatccatatctcgggttcgtctacacgtccttccagGAGCGAGCCACCACCATCTCTCACGGCAACACTGCTCGCCACGCCAAGGAGCACGGAGACCACAAGCTCGCGTGTTTGCGGCCTCATCGCAGCCGACGAG
|| | | ||| ||| | | | | | ||| | | | | | || || | ||| || |||| | |||||| |||||| | || |||||| | || || | |||||| |||||||| | ||||||||||| |||||| ||||||| ||||||||||| || ||||||||
tcgctgcagtgcatctagaaagttttactcaacacacccaaaatgtttggctagatttcaattcaatgttgtttgcttggttttggttgcaacttgcaagGATCCACGAACGGAGAACGACCCGTACATGGGGTTCATCTACACGACGTTCCAGGAGCGCGCCACCTCCATCTCCCACGGCAACACGGCGCGCCACGCGG------------------------------------------------------
upper sequence: EFJ28408 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os01g69080.1 (Oryza sativa), 3'ss of exon 2
-----------------gtacttgatcggttctggaatggtaaagagccagagtttcttctttctcaggaactccaaagttcgcgtttccatccttgcaggatcctcagaccgagaacaatccatatctcgggttcgtctacacgtccttccagGAGCGAGCCACCACCATCTCTCACGGCAACACTGCTCGCCACGCCAAGGAGCACGGAGACCACAAGCTCGCGTGTTTGCGGCCTCATCGCAGCCGACGAG
| | | |||| || | ||| | || | || | | | | | | | | | || ||||| ||| ||| ||||||||||| ||||| || ||| ||||||| |||||||| ||||| || ||| |||||| || || |||||||||||||| ||||
ttttgctctgttctattctgttctgttcacattggactgtttaagtggcaattgagcagagaaatctgtagcacttactcttttgctgcatcatttccagGACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTCCAAGAGCGTGCGACCTTCATCTCACATGGGAACACTGCTCGCCATGCCA------------------------------------------------------
upper sequence: EFJ28408 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G027673_T02 (Zea mays), 3'ss of exon 2
----gtacttgatcggttctggaatggtaaagagccagagtttcttctttctcaggaactccaaagttcgcgtttccatccttgcaggatcctcagaccgagaacaatccatatctcgggttcgtctacacgtccttccagGAGCGAGCCACCACCATCTCTCACGGCAACACTGCTCGCCACGCCAAGGAGCACGGAGACCACAAGCTCGCGTGTTTGCGGCCTCATCGCAGCCGACGAG
||| || | | | |||| | | | | | | | || | || ||| | |||||||||| |||| |||| || || || | || |||||||||||||| ||||||||||| |||||| |||||| ||||||||||| || ||||||||||
gtgagtaattatttaccttta-aatgatgggtggttgatgcatgaacgtacgcacg-----catgacgtacgtacaaacaaatgcagGATCCCAAGACGGAGACGAACCCGTACATGGGCTTCGTCTACACGTCGTTCCAGGAGCGCGCCACCTTCATCTCCCACGGCAACACGGCGCGCCACGCCA------------------------------------------------------
upper sequence: EFJ28408 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM5G852502_T01 (Zea mays), 3'ss of exon 2
---------gtactt-gatcggttctggaatggtaaagagccagagtttcttctttctcaggaactccaaagttcgcgtttcca-------tccttgcaggatcctcagaccgagaacaatccatatctcgggttcgtctacacgtccttccagGAGCGAGCCACCACCATCTCTCACGGCAACACTGCTCGCCACGCCAAGGAGCACGGAGACCACAAGCTCGCGTGTTTGCGGCCTCATCGCAGCCGACGAG
|||| | | |||| | | || | || | | |||| | || | | || | || ||||||||| ||| ||||| ||||| ||||| || ||| ||||||| |||||||| ||||| || ||| |||||| ||||| ||||||||||| |||||||
atcttttgttcacttcgtttttttcttctttaaatataggctacttcttataaatatgtaggaggactaatatgtactttctttactgtgtccttttcagGATCCTAGGACTGAGAATAATCCTTATCTTGGTTTCATCTACACCTCCTTCCAAGAGCGGGCGACCTTCATCTCACACGGGAACACTGCTCGTCACGCCA------------------------------------------------------
upper sequence: EFJ28408 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G180399_T01 (Zea mays), 3'ss of exon 2
------------------gtacttgatcggttctggaatggtaaagagccagagtttcttctttctcagga--actccaaagttcgcgtttcca--tccttgcaggatcctcagaccgagaacaatccatatctcgggttcgtctacacgtccttccagGAGCGAGCCACCACCATCTCTCACGGCAACACTGCTCGCCACGCCAAGGAGCACGGAGACCACAAGCTCGCGTGTTTGCGGCCTCATCGCAGCCGACGAG
|||||| | || || | || | | || | | |||| | | ||||| | | | || ||||||||| ||| ||||| ||||| ||||| || ||| ||||||| |||||||| ||||| || ||| |||||| || || ||||||||||| || ||||
gatgattatttctcttttgtactttgtttttttaagatctat-----gctactgattataactatgtaggactaatatgtagttcctttactgagtccttttcagGATCCTAGGACTGAGAATAATCCTTATCTTGGTTTCATCTACACCTCCTTCCAAGAGCGGGCGACCTTCATCTCGCATGGGAACACTGCTCGTCATGCCA------------------------------------------------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggatcctcagaccgagaacaatccatatctcgggttcgtctacacgtccttccagGAGCGAGCCACCACCATCTCTCACGGCAACACTGCTCGCCACGCCAAGGAGCACGGAGACCACAAGCTCGCGTGTTTGCGGCCTCATCGCAGCCGACGAG
cgtccttcc CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttgatcggttctggaatggtaaagagccagagtttcttctttctcaggaactccaaagttcgcgtttccatccttgcaggatcctcagaccgagaacaatccatatctcgggttcgtctacacgtccttccagGAGCGAGCCACCACCATCTCTCACGGCAACACTGCTCGCCACGCCAAGGAGCACGGAGACCACAAGCTCGCGTGTTTGCGGCCTCATCGCAGCCGACGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT