Sequence
atgc intronic sequence ATGC exonic sequence...atagatagctgcattcgaggatatctttccctttcggatgtgcctttgcgaattgagtactttgcgttgtggtgattgatggtggcgctggaactaccagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGCCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ12750 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ12750 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
--------------------------------atagata-gctgcattcgaggatatctttccc---tttcggatgtgcctttgcgaattgagtactt-tgcgttgtggtg--attgatggtggcgctg--gaactaccagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGCCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT
| | | | ||| || | | || | | || | | | | || ||| || || || || || | || | ||| || || ||||| ||| | |||||||| ||||| || || || ||||||||||||||||| |||| ||||| ||||| | |||||||||||||||||| | ||||
gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
upper sequence: EFJ12750 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G453565_T01 (Zea mays), 3'ss of exon 1
atagatagctgca---ttcgaggatatctttccctttcggatgtgcctttgcgaattgagtactttgcgttgtggtgattgatggtggcgctggaactaccagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGCCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT
||||| | ||| || | | | | || ||| ||| | ||| | | | | | | |||||||||| |||| || || || |||||||| |||||||| |||||||| |||||||| ||||| ||||| ||||||||||||| ||||||| ||||||||
-gtctcagctgtatatttcatacatggataactaataaaaaccggcatttatt--ttgtttccttcatcaatcaatcaataaatcaaatgtggtccactccagGTGGATCTGGTGGGCGGCTACTACGACGCCGGCGACAACGTCAAGTTCGGCCTGCCGATGGCGTTCACGGTCACCATGATGTCCTGGAGCGTCATCGAGT
upper sequence: EFJ12750 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G143747_T01 (Zea mays), 3'ss of exon 1
-----------------------atagatagctgcattcgaggatatctttccctttcggatgtgc-ctttgc-gaattgagtac--tttgcgttgtggtgattgatggtggcgctggaactaccagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGCCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT
| | ||| | || || | | || | | | || | | | || | ||| || ||| ||| |||| || || | | |||||||| | || |||||||| |||||||| |||||||| || ||||| |||||||||||||| ||||| | ||||||||||||||| || | | ||||
gtatgcacaacgcgtctctcgttgcattaattagcaagcaagcat-tgtgaccatggcagctgggttcgtcgctgtgctgaacacgatttttgttttggttcttttatgttttgtctcgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT
upper sequence: EFJ12750 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA08G02610.1 (Glycine max), 3'ss of exon 1
atagatagctgcattcgaggatatctttccctttcggatgtgcctttgcgaattgagtactttgcgttgtggtgattgatggtggcgctggaactaccagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGCCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT
| || || | ||||| |||| | | | | | |||| || || | || || ||| || | | | ||||||||| | ||||||||||| || || || || |||||||| ||||| || | |||||||| || ||| | || ||||||||||||||| ||| || |
--------gtaagtttaagaac-tcttttactttag--tttactcacccaaattc----tttctagtcctagtt-ttcatgttgatgttaaattatgcagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT
upper sequence: EFJ12750 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA05G36930.1 (Glycine max), 3'ss of exon 1
atagatagctgcattcgaggatatctttccctttcggatgtgcctttgcgaattgagtactttgcgttgtggtgattgatggtggcgctggaactac-cagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGCCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT
| || | | ||| || | | | | | | || | || ||| | || | | | || || ||||||||| | ||||||||||| || || || || |||||||| ||||| || | |||||||| || ||| | || ||||||||||||||| ||| || |
-------gtaagcttttcaactctttttttagtttagtttagtttctc--actttcctcacccaaattcaggttacaaattattgatgttaaattatacagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT
upper sequence: EFJ12750 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv02s0025g01380.t01 (Vitis vinifera), 3'ss of exon 3
--------atagatagctgcattcgaggatatct------ttccctttcggatgtgcctttgcgaattgagtactt-------------tgcgttgtggtgattgatggtggcgctggaactac-cagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGCCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT
|| || || | || ||| | | | | | | | | |||||| | || || |||| || || | | || || |||||||| |||| ||||| ||||| || || || |||||||| ||||||||||| |||||||| |||||| | || |||||||| |||||| | ||||
gtaagttcattttccactccaactcaaaatttctgaaaagcccattgtggaacaagacaattataattgaattattccatacaaccaaatgtgttgaagttttttgctataatctttgagttatgtagGTGGATCTGGTGGGAGGATATTATGATGCAGGTGACAATGTGAAGTTTGGCCTACCCATGGCATTCACCGTTACAATGATGTCATGGAGCATAGTGGAGT
upper sequence: EFJ12750 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S176_127V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------------atagatagctgcattcgaggatatctttccctttcggatgt-gcctttgcgaattgagtactttgcgttgtggtgattgatggtggcgctggaactaccagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGCCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT
|||| | | | || | | | |||| | | | |||| | ||||| || | | ||| | | | || |||||||| ||||||| || |||||||| || || |||||||||||||||||| |||| |||| ||||| | |||||| |||||||||| | | ||||
gtaagaccttcgtttcgcgttctagatgggtgactgttttatcttaagcatagaaaaagttgtgaagaggatgtagacatgctcgccagctgacaattaaatatgatatatgtaggatatagtcattggttcatttgctttacgattatttgtacttgtaatg-------tagGTGGATCTGGTTGGTGGTTATTACGATGCTGGTGACAATGTCAAGTTTGGCTTGCCTCTGGCATTCACTGTTACCATGCTGTCGTGGAGTGTTCTTGAGT
upper sequence: EFJ12750 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S53_97V6.1 (Physcomitrella patens), 3'ss of exon 1
atagatagctgcattcgaggatatctttccctttcggatgtgcctttgc---gaattgagtactttgcgtt--gtggtgattgatggtggcg-ctggaactaccagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGCCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT
| | || || || | | | ||||| || | || | | ||| | || || ||| | | ||| | || | || |||||||| || || ||||||||||| |||| || || |||||||| ||||||||||||||| | || |||| | ||| |||
------gatcggttgttagaatgcctctgctaatatattgtgcgattattttgtgttaattttttttttatcagtatgcatcagccgtgttatccttcgttggcagATTGACCTTACGGGCGGGTATTATGATGCTGGCGACAATGTGAAGTACGGACTTCCCATGGCATTCACCATCACCATGCTCTCCTGGAATGTCATTCAGT
upper sequence: EFJ12750 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S149_10V6.1 (Physcomitrella patens), 3'ss of exon 2
-------atagatagctgcattcgaggatatctttccctttcggatgtgcct------------ttgcgaattgagtactttgcgttgtggtgattgatggtggcg----ctggaactac-cagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGCCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT
| | |||| |||| ||| | | | |||| | | |||| || | | || | || |||| | ||| || || |||| | ||| || |||||||||||||| |||||||| ||||| || ||||| ||||||| || ||||| ||| | || ||||||| || || |
gtatgtcgcacactctccaattccaggagcatttttgcaatgagctgtgagtagagcgagaatgtcgcgagggaaggtgccaggttgctgataatgtgcggtgttggtttctgtgtctctgtagCTGGACCTCTCTGGGGGCTATTACGACGCGGGAGACAATGTGAAGTTCGGTCTGCCGATGGCCTATACTATCACGATGCTCTCATGGAGCGTAATTGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcgaattgagtactttgcgttgtggtgattgatggtggcgctggaactaccagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGCCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT
gattgat putative branch site (score: 4)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atagatagctgcattcgaggatatctttccctttcggatgtgcctttgcgaattgagtactttgcgttgtggtgattgatggtggcgctggaactaccagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGCCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - -tagctgc
- - - - - - - - - - -tatcttt
- - - - - - - - - - - - - - ccctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgcgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggcgct