Sequence
atgc intronic sequence ATGC exonic sequencegtttgagaaatatgatacttcctttcatgctcgtgttgctgatttgtttgttctagGCACATATTGGGCTATCCATGGGAATTGTAGGCACTGAAGTCGCAAAGGAAAGCTCAGACATTATTATTCTGGATGATAACTTTGCATCAGTTGTCAAA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ15121 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ15121 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 8
----------------------------------------------------------------------------------gtttgagaaatatgatacttcctttcatgctcgtgttgctgatttgtttgttctagGCACATATTGGGCTATCCATGGGAATTGTAGGCACTGAAGTCGCAAAGGAAAGCTCAGACATTATTATTCTGGATGATAACTTTGCATCAGTTGTCAAA
| | | | |||| | || | | | | | | | | |||||| | ||||| || | ||||| || ||| || ||||| || || ||||||||||| || |||||||||||||| || ||||| |||||||| ||
gtacatacataattgggaattttgttttgaacaaataaaaggataaacataatggttttatttcaatcagatgaagacaatcgatcatgcatgttgatgcacatttctaattttgatctcttattcctcctaatttagGCAGACATTGGTCTTGCTATGGGTATCCAAGGAACAGAAGTAGCTAAAGAAAGCTCAGATATAATTATTCTGGATGACAATTTTGCTTCAGTTGTAAAG
upper sequence: EFJ15121 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 24
------------------------------------------gtttgagaaatatgatacttcctt--tcatgctcgtgttgctgatttgtttgttctagGCACATATTGGGCTATCCATGGGAATTGTAGGCACTGAAGTCGCAAAGGAAAGCTCAGACATTATTATTCTGGATGATAACTTTGCATCAGTTGTCAAA
|||| ||| | || | | | | |||||| | || | || ||||| ||||||| || || ||||| || ||| |||||||| ||||| ||||||||||| ||||| || || || ||||||||||||||||| || ||
catctgtttggttgtcatgttccatttattaaaataattcctgtttactaaaaagaatcttgttatagttaatctcgtgctttactattttgaattttagGCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAG
upper sequence: EFJ15121 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 26
---------------------------------------------gtttgagaaatatgatacttcctttcatgct-cgtgttgctgatttgtttgttctagGCACATATTGGGCTATCCATGGGAATTGTAGGCACTGAAGTCGCAAAGGAAAGCTCAGACATTATTATTCTGGATGATAACTTTGCATCAGTTGTCAAA
||| | | | | || | || || | || || || || | | | |||||| ||||||| || || ||||| || ||| || ||||| ||||| ||||| ||||| ||||| || |||||||||||||||||||||| || ||
gggtaccaaatccgaaactggaaataaactgggatcaaaaatgtaattttaccatttttttattatagtttatacaatgttttacta--ttatgtaatttagGCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTTGCAAAAGAAAGTTCAGATATTATAATCTTGGATGATAACTTTGCATCAGTAGTAAAG
upper sequence: EFJ15121 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 26
------------------------------------gtttgagaaatatgatacttccttt--catgctcgtgttgctgatttgtt------tgttctagGCACATATTGGGCTATCCATGGGAATTGTAGGCACTGAAGTCGCAAAGGAAAGCTCAGACATTATTATTCTGGATGATAACTTTGCATCAGTTGTCAAA
|||| || ||| || || | || || | | || ||| | | | |||||| ||||||| || || ||||| || ||| || ||||| ||||| ||||| ||||| ||||| || |||||||||||||||||||||| || ||
aaagttgaaatttaaaattcattattaaaacctagagtttatcaattatattaatttccttattatagttgatacagtgctttactattatgtaatttagGCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTTGCAAAAGAAAGTTCAGATATTATAATCTTGGATGATAACTTTGCATCAGTAGTAAAG
upper sequence: EFJ15121 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 27
------------------------------------------gtttg--agaaatatgatacttcctttcatgctcgtgttgctgatttgtttgttctagGCACATATTGGGCTATCCATGGGAATTGTAGGCACTGAAGTCGCAAAGGAAAGCTCAGACATTATTATTCTGGATGATAACTTTGCATCAGTTGTCAAA
|||| | ||| || | || | | || ||| | || | | || |||||| ||||||| || || ||||| || || |||||||| ||||| ||||||||||| ||||| || || || || |||||||||||||| || ||
attggttgtcatgctccattctctaatattaaaataattcctgtttactaaaaagatccttgttatagttaatcttgtgctttactattttgtattttagGCAGATATTGGTCTTTCTATGGGCATCTCCGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGACAACTTTGCATCAGTAGTAAAG
upper sequence: EFJ15121 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 26
------------------------------------------gtttgagaaatatgatacttcct--ttcatgctcgtgttgctgatttgtttgttctagGCACATATTGGGCTATCCATGGGAATTGTAGGCACTGAAGTCGCAAAGGAAAGCTCAGACATTATTATTCTGGATGATAACTTTGCATCAGTTGTCAAA
| || | || || | ||| | | || || |||| || | | || |||||| |||| || || || ||||| ||| ||| |||||||| ||||| |||||||||||||| ||||| |||||||||||||||| |||||||| ||
ttatggctgtagagtttggatgttgtttttccatcttcagcaggttcataatgttgtttctttgtaatgattgatcaggttgtatcattttctattgtagGCAGATATAGGTCTCTCTATGGGCATTCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGACATCATTATCTTGGATGATAACTTTGCCTCAGTTGTAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgagaaatatgatacttcctttcatgctcgtgttgctgatttgtttgttctagGCACATATTGGGCTATCCATGGGAATTGTAGGCACTGAAGTCGCAAAGGAAAGCTCAGACATTATTATTCTGGATGATAACTTTGCATCAGTTGTCAAA
tgctgat putative branch site (score: 3)
tttgttct putative PPT
aaatatgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgagaaatatgatacttcctttcatgctcgtgttgctgatttgtttgttctagGCACATATTGGGCTATCCATGGGAATTGTAGGCACTGAAGTCGCAAAGGAAAGCTCAGACATTATTATTCTGGATGATAACTTTGCATCAGTTGTCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA