Sequence
atgc intronic sequence ATGC exonic sequencegtagcctgtgatgtttctaagttgttcttcccaaggatttggagctcactctctcgcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ19598 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 3'ss of exon 2
---------------------------------------gtagcctgtgatgtttctaagttgttcttcccaaggatttggagctcactctctcgcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAA
|| | | | ||||| | ||| | | | | | | | | ||| || || ||||| || ||||||||||||||||| || || |||||||| || |||||||| || ||||||| || ||||| ||||| || ||
gtccggctctctcttttttttttacatatttttactgttatatctcagcttagcctgagcttgttttatccatatcaattcatttgttacaactaatggtcctacagGTTCTTCTATGCCTCAAGTGCATGCATTTACCCTGAATTCAAGCAGCTTGAAACTAACGTTAGCCTGAAGGAATCTGATGCCTGGCCTGCTGAG
upper sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os11g37890.2 (Oryza sativa), 3'ss of exon 2
--------------------------------gtagcctgtgatgtttctaagttgttcttcccaaggatttggagctcactctctcgcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAA
| | | ||| | | || ||| || | | | | || ||| || || |||||||| || ||||| || || ||||| || |||||||||||||| ||| || || ||||||||||||||||| ||||| |||||
aaccctagaattcctcaaaacagagcatttactttaacaatcctgtcatgttatcatcactcagaagaatcatcattttggttattttttttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGACACTGTAGTTAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
upper sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os11g37890.3 (Oryza sativa), 3'ss of exon 2
--------------------------------gtagcctgtgatgtttctaagttgttcttcccaaggatttggagctcactctctcgcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAA------
| | | ||| | | || ||| || | | | | || ||| || || |||||||| || ||||| || || ||||| || |||||||||||||| ||| || || ||||||||||||||||| ||||| |||||
aaccctagaattcctcaaaacagagcatttactttaacaatcctgtcatgttatcatcactcagaagaatcatcattttggttattttttttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGACACTGTAGTTAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAGGTTTCT
upper sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G124434_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------gtagcctg--tgatgtttctaagttgttcttcccaagga-----tttggagctcactctctcgcttgg--cttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAA
||| || ||||| | | || || ||| || || | | | || || | || ||| || || ||||| || ||||||||||||||||| ||||| |||||||| || || || ||||| |||||||| || ||||| ||||| || ||
gtatatatacaaatatattgccacttcattttctttctggctggtgaataacttcccaagtaatctagctgatgctatttgactgaagttttcaaagaacctattcatgcataatagtatcattttggtctggcagGTTCTTCTATGCCTCGAGTGCATGCATTTACCCTGAGTTCAAGCAGCTTGACACAAATGTGAGCTTGAAGGAATCTGATGCCTGGCCTGCTGAG
upper sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 1
-----------------------------------------gtagcctgtgatgtttcta-agttgttcttcccaaggatt--tggagctcactctctc-----gcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAA
| | | ||| | | | |||| | | | || | | | || | |||||| ||||||||||| || ||||| || || ||||| || ||||| ||| |||| ||||| ||||| ||||||||||| |||||||||||||| ||
gttagccatcatgcacatcatttcaattatttgtttttggaccaaacatttatgatgcggtggctgttttgattagatgatgatgtgttttatgcgttctgaaaaatatttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG
upper sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 2
------------------------------------------gtagcctgtgat-gtttctaagttgttcttcccaaggatttggagctcactctctcgcttggcttcc--agATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAA
| || || || || | || || | | || | ||| || | | | | || || || ||||||||||| || ||||| || || || || || || |||||| ||||||| || ||||||||||||||||| ||||| ||||| || ||
gtcattcattttgaacaaacatgtgttattatgtcactttcaattgcatgatatagtctttatgtcgc-cgtcatagtgatc-----cttgttttttggtttattttttttagGTTTTTTTATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAGCAGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG
upper sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------gtagcctgtgatgtttctaagtt---gttcttcccaaggatttggag---ctcactctctcgcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTA---ACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAA
|| || | | || | || ||| | || | || | | | | | | ||| || || || |||||||| || ||||| || || || || |||||||||||| ||||||||| | ||||| ||||||||||||||||| ||||| |||||
gttagttagattttgttttcttcggttttcgcagtttacggtttcttaaaacaagttaaaaagattggattttttgtttgcttt--agGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
upper sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv14s0030g02180.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------------------------------------------------------gtagcctgtgatgtttctaa---gttgttct--tcccaaggattt----ggagctcactctctcgcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAA
| || | || | || |||| || |||| ||| || ||| | || | | | | | | | | ||| || || ||||| || ||||| ||||| ||||| || ||||||||| |||| ||||| ||||| ||||||||||| ||||||||||| |||||
gtttgttgtcttcaatttgttctatcctggctttgactaagttctccatttgatatgaaaattggtttcatgtactcagcatttatctgtctaggagac-gtaaatttactaatgaatttttctggtcctgagaattctctaatatctgattattccacattg--tgcagGTTCTTCTATGCCTCTAGTGCTTGCATCTACCCTGAATTTAAGCAGTTGGAAACTAATGTGAGCTTGAAGGAGTCTGATGCATGGCCTGCAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctaagttgttcttcccaaggatttggagctcactctctcgcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAA
agctcac putative branch site (score: 3)
ctcactctctcgctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcctgtgatgtttctaagttgttcttcccaaggatttggagctcactctctcgcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG