Sequence
atgc intronic sequence ATGC exonic sequence...tcctccagtgtacttaggtgagtaatctatcgaatttttctcgattgtggagctaaacttttggtggttttcttttctttttttcttgcgttttgcgtagGGGGGTATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ17692 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ17692 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os06g44750.1 (Oryza sativa), 3'ss of exon 4
-----------tcctccagtgtacttaggtgagt-aatctatcgaatttttctcgatt-gtggagctaaacttttggtggttttcttttctttttttcttgcgttttgcgtagGGGGGTATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
| | | || | | ||| | || || || ||| || | || | || || || || ||| ||| || |||||| |||||||||||| |||||||||||||| || || || || ||||||||||| || || || || || ||||| ||
gtatgtcgtcattatttgcaacatctatatatcttaattagttagtttcttttccattcgttcaccttgagacttactgtaaaagttgggggattaaacaaaacttt---cagGAGGTTATGATAAGGAGGAGAAGGCCGCAAGAGCTTACGACCTCGCCGCCCTAAAGTACTGGGGTCCAACCACCACGACGAACTTCCCT
upper sequence: EFJ17692 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G366434_T01 (Zea mays), 3'ss of exon 3
tcctccagtgtacttaggtgagtaat--ctatcgaatttttctcgat-tgtggagctaaac-ttttggtggttttcttttctttttttcttgcgttt--------tgcgtagGGGGGTATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
| || | | | | || | | |||||| | | | | | || || |||| | | || | | | | | |||| || ||||| |||||| ||||||||||| ||||||||| |||||||||||||||| ||||| |||||||||| ||||| || ||
---tggtatgcattcaccttagctcctgcccttacatttttgttgttgtatagatcttcctattttaacaatcattttgctatgccattgtatatccactgtaTACACTTAGGTGGCTATGACAAGGAGGACAAGGCAGCAAGGGCTTACGATTTGGCAGCTCTCAAGTATTGGGGCACTACGACAACAACAAATTTCCCT
upper sequence: EFJ17692 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G366434_T02 (Zea mays), 3'ss of exon 3
tcctccagtgtacttaggtgagtaat--ctatcgaatttttctcgat-tgtggagctaaac-ttttggtggttttcttttctttttttcttgcgttt--------tgcgtagGGGGGTATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
| | || | | | | || | | |||||| | | | | | || || |||| | | || | | | | | |||| || ||||| |||||| ||||||||||| ||||||||| |||||||||||||||| ||||| |||||||||| ||||| || ||
-cttggtatgcattcaccttagctcctgcccttacatttttgttgttgtatagatcttcctattttaacaatcattttgctatgccattgtatatccactgTATACACTTAGGTGGCTATGACAAGGAGGACAAGGCAGCAAGGGCTTACGATTTGGCAGCTCTCAAGTATTGGGGCACTACGACAACAACAAATTTCCCT
upper sequence: EFJ17692 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G139082_T01 (Zea mays), 3'ss of exon 4
------------------------------------tcctccagtgta-cttaggtgagtaatcta---tcgaattt---ttctcgattgtggagctaaacttttggtggttttcttttctttttttcttgcgttttg---------------cgtagGGGGGTATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
| |||| | | ||| || | | || || ||| || || | | | || |||| | | || | ||| | || ||||| || ||||| |||||||||||| || ||||||||||| || || || |||||||||||||||||||| || || || ||||| |||
gtacgtatatactacgtcaacttccactacacccagtactccgtttcagcttcagttggacacttacattcaaatcaacattatcaaatcaaaatgtatttttttagatatattagaaagtgtttggaactaactgtggaaagggggaaaaactgtagGAGGCTATGACAAGGAGGAGAAGGCGGCTAGAGCTTACGACCTCGCCGCGCTCAAGTACTGGGGGCCTACAACCACGACCAACTTCCCG
upper sequence: EFJ17692 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G399072_T01 (Zea mays), 3'ss of exon 3
---------tcctccagtgtacttaggtgagtaatctatcgaatttttctcgattgtggagctaaacttttggtggttttcttttcttt--ttttcttgcgttttgcgtagGGGGGTATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
| |||| ||| |||||||| | || | || ||| | || | | | ||||| | | || | | |||| || ||||| |||||||||||| || || ||||| || ||||||||||||||||||||||| || |||| | ||| || |||
tcaacaacgacgagcagtctacctaggtgagcta-ctgcaagcctcctcctagctgtttgttgctccacatgctcaccaccatgtctttgctatgactgtgGCTGCTCTAGGCGGCTATGACAGGGAGGAGAAGGCTGCGAGGGCTTATGACCTGGCAGCTCTCAAGTACTGGGGCCCCTCGACTCACATAAATTTCCCG
upper sequence: EFJ17692 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G399072_T03 (Zea mays), 3'ss of exon 3
tcctccagtgtacttaggtgagtaatctatcgaatttttctcgattgtggagctaaacttttggtggttttcttttcttt--ttttcttgcgttttgcgtagGGGGGTATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
||||| | || | || ||| | || | | | ||||| | | || | | |||| || ||||| |||||||||||| || || ||||| || ||||||||||||||||||||||| || |||| | ||| || |||
-----------------gtgagcta-ctgcaagcctcctcctagctgtttgttgctccacatgctcaccaccatgtctttgctatgactgtggctgctctagGCGGCTATGACAGGGAGGAGAAGGCTGCGAGGGCTTATGACCTGGCAGCTCTCAAGTACTGGGGCCCCTCGACTCACATAAATTTCCCG
upper sequence: EFJ17692 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA17G07010.1 (Glycine max), 3'ss of exon 4
--tcctccagtgtacttaggt---gagtaatctatcgaattttt-ctcgattgtggagctaaacttttggtggttttcttttctttttttcttgcgttttgcgtagGGGGGTATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
| | | | ||| | || | ||| | | || | | | | | | | |||| || |||| | ||| |||||| || ||| |||| || ||||| |||||| |||||||| |||||||| ||||| |||||||||||||||||||| || || || || || ||||||||
ttgattgcgcatttcctagattcagattcttctctaggataatcattttagtcaaaaaatgacttttttgttgtttcttcttcctttttt--tgtgtt----atagGTGGTTATGACAAGGAGGATAAGGCAGCCAGAGCTTATGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACTAACTTTCCT
upper sequence: EFJ17692 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA13G00950.1 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------------------------------tcctccagtgtacttaggtgagtaatctat-cgaatttttctcgattgtggagctaaacttttg-------gtggttttcttttctttttttcttgcgttttgcgtagGGGGGTATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
| || | | || | | || | ||| ||||| | ||| | ||| | || ||| |||||| || || | | | |||| || ||||| ||| || |||||||| || ||||||||||| |||||||||||||||||||| || || || || || ||||||||
gtgagtatatcattactaccttgacctcatcattttgttttaccatcacaaaccacatacatatatacaactgttcatttatgatcatcaatttgattgcgcatttcccagattcagattcttctctagctaggataatcattttagtcaaaaaatgacttttgtttcttcttccttttctgtgt-tatagGTGGTTATGACAAGGAAGATAAGGCAGCCAGGGCTTACGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACCAACTTTCCC
upper sequence: EFJ17692 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv11s0052g00840.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------tcctccagtgtacttaggtgagtaatctatcgaatttttctcgattgtggagctaaacttttggtggttttcttttctttttttcttgcgttttgcgtagGGGGGTATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
| | || ||| | | | || | ||| | || | || | ||| | | ||| | || ||| || | || | | ||| ||||||||| ||| ||||||||||| |||||||| ||||| || ||||| ||||||||||| || || || || || ||||| ||
gtgagtaggatctcatctcgtggtcttgtcctgaatcatgatttttcactgt---tgaataaaagattc-tgatattccttcaagttttagattctcattttggatcaatttttatttatttatttattttttgtttgcagGTGGGTATGATAAGGAAGAGAAGGCAGCTAGAGCTTATGATCTCGCCGCTCTTAAGTACTGGGGTCCGACCACCACCACTAACTTCCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtggagctaaacttttggtggttttcttttctttttttcttgcgttttgcgtagGGGGGTATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
agctaaa putative branch site (score: 3)
ttttcttttctttttt putative PPT
ttttcttttctttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcctccagtgtacttaggtgagtaatctatcgaatttttctcgattgtggagctaaacttttggtggttttcttttctttttttcttgcgttttgcgtagGGGGGTATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
tcctcca
- - - - tgtactt
- - - - - - - - - - - - - - - - - -ttttctc
- - - - - - - - - - - - - - - - - - - - - - - - ggagcta