Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgtacgatttttcttttcgtgtgtctctaaataagctgtgcctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATCTGTATAAAACAT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ14095 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 13
---------------------------------------------------gtaagtgtacgatttttcttttcgtgtgtctctaaataagc--tgtgcctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATCTGTATAAAACAT
| || || ||| || | || || | | | ||| | ||||||||| |||||||| |||||||||||||| || || || || || | || || ||||| || ||| | |||||| | || || || || || |||||||
gtaaggctcattactactttccatttctgcatcaacatgtcatattcatcaagatatgcacatctttgtcttggttttggacttatctcactcatatgctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT
upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 14
--------------------------------------------------------gtaagtgtacgatttttcttttcgtgtgtctctaaataagctgtgcctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATCTGTATAAAACAT
| | | |||| || || | ||| | | | | ||||||||| |||||||| |||||||||||||| || || || || || | || || ||||| || ||| | |||||| | || ||||| || || |||||||
gtaaggctcgttactactttgccatttcttcatcaatatgtcacattcatcaggatatgcacatccttatttttgttccgaacttatctgtctgcctctttctgctcacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAAGACCTTTACAAAACAT
upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 14
--------------------------------------gtaa--gtgtacgatttttcttttcgtgtgtctctaaataagctgtgcctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATCTGTATAAAACAT
| || || |||| || | | | | |||| ||| || ||||||| || ||||| || ||||| ||||| |||||||| || ||| ||||||| ||||||||||| ||||| || | || |||||| |||| |||| |
gtacacttatgatccatttgtcttgattttttaatattgcaatggttcacgagggttttggtagctgatatctattgtgcaattgcaatctatagGTTGTAGCATCTCAAGACTGGCCTGAAGTGACGAAATATGCCGGTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGT
upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
---------------------------gtaagtgtacgatttttcttttcgtgtgtctctaaataagctgtgcctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATCTGTATAAAACAT
|| ||| || || | | || | | | | || | | ||||||| |||||||| || ||||| ||||| || ||||| || ||| |||| || |||||||||||||| ||||| | || |||||| ||||||||||||
gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttct----tttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 12
------------------------------------------------gtaagtgtacgatttttcttttcgtgtgtctctaaataagctgtgcctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATCTGTATAAAACAT
||||| | || || || || || | ||| || |||| || ||||||||||| ||||| |||||||| ||||| ||||| | || || ||||| ||||||||||| || |||| |||||| | || || ||||
gtaaaatttctttaactgatatcatgcttcctagaaccttgtttttcctaaagtggttattgaggaactttgt-tgctgatagatt-gttgtattaattgtagGTAGTAGCTTCTCAGGACTGGCCTGAAGTCACAAAATATGCAGGATTGGTTTGTGCTCAGGCTCACAGACAGGAACTGATACAAGATTTATACAAGACAT
upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: PP1S173_134V6.1 (Physcomitrella patens), 3'ss of exon 13
--------------------------------------------------------------------------gtaagtgtacgatttttcttttcgtgtgtctctaaataagctgtgcctg---ttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATCTGTATAAAACAT
|| | || || | | ||| | | | | || | || |||||||| || || ||||||||||| || ||||| || ||||| ||| |||||||||||||| ||||| | ||||||||||| || || | ||| ||
gtaagtcttccttacctttgttagtgctattttgtttgaacgagacatggttcaaatcaataacgagtttccatgtcacagtttaatatgatactattatcttctttggttgacttccgcatttgtttgcagGTTGTGGCATCGCAGGATTGGCCTGAGGTCACCAAGTACGCTGGTTTAGTGTGCGCTCAAACTCACCGTCAAGAGTTGATTGCGGACCTATTCAAAGAAT
upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 12
----------------------------------------------------------------------------------------------------------gtaagtgtacgatttttcttttcgtgtgtctctaaataagctgt-gcctgt-tacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATCTGTATAAAACAT
|| | | | || | | | | ||| | || | | ||||| || ||||| ||||||||||| || ||||| ||||| || || | |||||||||||||||||| | || |||||||| || |||||||| ||| |
gtaagttactgtaaccaagcgattgcccccacttattaatagctgataagctatatgtatttaggtctcaattgagaagtgtcgcccttgattttgaattctcttaacgtgtacatagtgcgcacgatttcctggcgatga-cattttgtcgtctatatgcagGTGGTAGCTTCGCAGGATTGGCCTGAGGTCACTAAATATGCCGGATTGGTGTGCGCTCAAGCTCACCGTCAGGAGTTGATTCAGGATCTGTACAAAGAGT
upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: PP1S28_182V6.1 (Physcomitrella patens), 3'ss of exon 13
----------------------------------------------------------------------------------------gtaagtgtacgatttttcttttcgtgtgtctcta-----aataagctgtgcctgt-tacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATCTGTATAAAACAT
|| || | | | ||| || | || |||| | | ||| | ||||| || ||||| ||||||||||| || ||||| || || ||||| | ||||| |||||||||||| | || |||||||| || |||||||| || ||
gtaagtagctatcttcatgccatttgatcgtatagacatctgttctggatatctgatggctgtatgtttgcagagtcgcgtttgaattatactcttaggtctatacttagggtagtttcctggcaataatagtttttttttgtatgcagGTGGTAGCTTCGCAGGATTGGCCCGAGGTCACCAAGTATGCAGGGTTGGTGTGTGCTCAAGCTCACCGTCAGGAGTTGATTCAGGATCTGTACAAGGAATMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|169110846|gb|FE509329.1|FE509329EST: ATGTTACGCATCCTCATCCTGGAGAAGATTCGAGTCCCTCGATTGCAGCG GTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTG
genomic: ATGTTACGCATCCTCATCCTGGAGAAGATTCGAGTCCCTCGATTGCAGCGgtaagtgtac ... cctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTG
EST:
gi|169053755|gb|FE461522.1|FE461522EST: ATGTTACGCATCCTCATCCTGGAGAAGATTCGAGTCCCTCGATTGCAGCG GTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTG
genomic: ATGTTACGCATCCTCATCCTGGAGAAGATTCGAGTCCCTCGATTGCAGCGgtaagtgtac ... cctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTG
EST:
gi|169108089|gb|FE511032.1|FE511032EST: ATGTTACGCATCCTCATCCTGGAGAAGATTCGAGTCCCTCGATTGCAGCG GTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTG
genomic: ATGTTACGCATCCTCATCCTGGAGAAGATTCGAGTCCCTCGATTGCAGCGgtaagtgtac ... cctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTG
EST:
gi|169081815|gb|FE486414.1|FE486414EST: ATGTTACGCATCCTCATCCTGGAGAAGATTCGAGTCCCTCGATTGCAGCG GTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTG
genomic: ATGTTACGCATCCTCATCCTGGAGAAGATTCGAGTCCCTCGATTGCAGCGgtaagtgtac ... cctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTG
EST:
gi|169026895|gb|FE432387.1|FE432387EST: ATGTTACGCATCCTCATCCTGGAGAAGATTCGAGTCCCTCGATTGCAGCG GTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTG
genomic: ATGTTACGCATCCTCATCCTGGAGAAGATTCGAGTCCCTCGATTGCAGCGgtaagtgtac ... cctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTG
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
34 (upstream exon),
35 (downstream exon)
Score:
14ACGGAGGCTTCCTTTAGTAAGTGATACACCAACAATTATATTTGGAGCGGATGTTACGCATCCTCATCCTGGAGAAGATTCGAGTCCCTCGATTGCAGCGgtaagtgtac ... cctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATCTGTATAAAACAT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaagtgtacgatttttcttttcgtgtgtctctaaataagctgtgcctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATCTGTATAAAACAT
ctctaaa putative branch site (score: 14)
atttttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgtacgatttttcttttcgtgtgtctctaaataagctgtgcctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATCTGTATAAAACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA