Sequence
atgc intronic sequence ATGC exonic sequencegtaagcgcatttctctcttcgttctcttcgcgttttcgtgttcttcctccatagctagacttcaaagcctcactaaccgtttcattcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTTTGGCATTGTCCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC
Basic information
species | Selaginella moellendorffii |
transcript | EFJ28993 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ28993 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G102088_T02 (Zea mays), 3'ss of exon 2
-----gtaagcgcatttctctcttcgttctcttcgcgttttcgtgttcttcctccatagctagacttcaaagcctcactaaccgtttcattcat--tgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTTTGGCATTGTCCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC
|| | ||| || || || | | || || |||| | | | || | |||| || || |||||||||||||| |||||||||| || || || || || || ||||||||||||||||| |||||||||||||| || || |||| || || ||
cgaatgttttcttgtttgaagctaagtcagtcatgcatacaca-attgacaagttgtaaaaggactgaagatgtttacatattgtttttttaatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTTTGGCATTGTGCTGTGGGAGCTCATAACTGGCATGCTCCCTTTTGCTAAT
upper sequence: EFJ28993 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G156013_T01 (Zea mays), 3'ss of exon 2
-gtaagcgcatttctctcttcgttctcttcgcgttttcgtgttctt----cctccatagctagacttcaaagcctcactaaccgtttcatt-cattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTTTGGCATTGTCCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC
| | ||| ||| || | | | | | | | || || | | | | || | |||| | ||||||||||||||| ||||| |||| || || || || || || ||||||||||||||||| |||||||||||||| || || |||| || || |||
ttttttcttgtttgaatctgagtcattcatacatacacatttgacaaaggttataaaaggaggattgaagatgtttacatattgttttttaatcttgcagAGAGATGATTCAGCATAGGCCATATGACCAGAAAGTTGATGTCTACAGCTTTGGCATTGTGCTGTGGGAGCTCATAACTGGCATGCTCCCTTTTGCTAAC
upper sequence: EFJ28993 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA05G36540.2 (Glycine max), 3'ss of exon 2
-----gtaagcgcatttctctcttcgttctcttcgcgttttcgtgttcttcctccat--agctagacttcaaagcctcactaaccgtttcattcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTTTGGCATTGTCCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC
|| ||| | || || |||| || | | | || | | | | | | | | || | ||||| |||||||||||||| |||| ||||||||| || ||||| || || |||||||| ||||| || ||||| |||||||| || |||| || || ||||||
aatgcagaaattcatgattaattttaactgttttatatttttgtttacaaaattaatttgttttggtatttagattttgttgtttgctg-atctactgcagGGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTTTGGGATTGTTCTATGGGAACTCATCACTGGTATGCTTCCATTTCAGAAC
upper sequence: EFJ28993 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA08G03010.2 (Glycine max), 3'ss of exon 3
-----gtaagcgcatttctctcttcgttctcttcgcgttttcgtgttcttcctccat--agctagacttcaaagcctcactaaccgtttcattcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTTTGGCATTGTCCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC
|| ||| | || || || | || | | || | | | | | | | || | ||||| |||||||||||||| |||| ||||||||| || ||||| || || |||||||| ||||| || ||||| ||||| || || |||| || || ||||||
aatgcagaaattcataattagttttaagtgttttatattcttgtttaaaaaattaatttgatgtggtatttagattttgttgtttgctg-atctactgcagGGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTTTGGGATTGTTCTATGGGAACTCATTACCGGTATGCTTCCATTTCAGAAC
upper sequence: EFJ28993 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT4G31170.1 (Arabidopsis thaliana), 3'ss of exon 3
-------gtaagcgcatttctctcttcgttctcttcgcgttttcg-tgttctt-----cctccata-gctagacttcaaagcctcactaacc-gtttcattcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTTTGGCATTGTCCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC
| | || || | | | | || || || | | ||| ||| | | | | || | | | | | ||| || ||||||||||||||||||||||| | ||||| || || |||||||| || || ||||| || || ||||||||| | || ||||| || ||||||||||||||
gtaagttgaataaatatctcgttttccatccttgtcttgtccttaataaccttatatatctctgcaagtcatatttagacactatattcccttattttgatcgatgcagAGAGATGATCCAGCACAGACCCTACACTCAAAAAGTGGACGTGTATAGTTTTGGAATCGTGCTGTGGGAGTTGATTACAGGTCTGTTACCGTTCCAGAAC
upper sequence: EFJ28993 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv04s0008g03020.t01 (Vitis vinifera), 3'ss of exon 2
------gtaagcgcatttctctcttcgttctcttcgcgttttcgtgttcttcctccatagctagacttcaaagcctcactaaccgtttcattcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTTTGGCATTGTCCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC
| | || | || | | | ||| | || | || | | || | | | |||| | || |||||||||||||||||||||||||| ||||| || ||||| || || ||||||||||| |||||||||||||||||||||||||| ||||| || |||||||||
catgaaacaggaccaccttgtaatttttgttgtagattcttttatatttataagtgattcattggttttgattttttgatgtgcgttacttttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTTTGGAATTGTCCTGTGGGAGCTCATCACAGGCTTGCTTCCCTTCCAGAAC
upper sequence: EFJ28993 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv11s0065g00140.t01 (Vitis vinifera), 3'ss of exon 1
--gtaagcgcatt----tctctcttcgttctcttcgcg--ttttcgtgttcttcctccatagctagacttcaaagcctcactaaccgtttcattcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTTTGGCATTGTCCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC
| | ||| || | ||| ||| || ||| |||| | | | | | ||| | || | | | |||| ||||| ||||||||||||||||||| ||||||||| || || ||||| || |||||||| || || || ||||| |||||||| || |||| || |||||||||
tctcatacttattaaggccttagtacgtgtactttgctacatttattgttataaattttcaacctg-cttgagtgcatt-ttcatattttctcaacctgcagGGAGATGATCCAGCACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTTTGGGATCGTTCTTTGGGAACTCATCACTGGGATGCTTCCATTCCAGAAC
upper sequence: EFJ28993 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S120_103V6.1 (Physcomitrella patens), 3'ss of exon 2
--------gtaagcgcatttctctcttcgttctcttcgcgttttcgtgttcttcctccatagc-tagacttcaaagcctcactaaccgtttcattcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTTTGGCATTGTCCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC
| | ||| | || || | ||| | | | ||| || || | | ||| | | || | | ||||| |||||||||||||||| | ||||| ||||| |||||||| ||||||||||| | ||| | |||||||| | ||||| || | || || || ||
ctgattcaggtgttgtgttttgggcatctttagaggttcaggttcaaatgttcgattcattgcatattagtgagagctaagttggaccttgga---actgcagGGAGATGATCCAGCACAAACCTTACAATCACAAAGTGGACGTCTACAGCTTTGGTGTGGTCTTATGGGAGCTTGTGACAGGCCTGTTGCCCTTTCAAAAT
upper sequence: EFJ28993 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S69_199V6.2 (Physcomitrella patens), 3'ss of exon 3
---gtaagcgcatttctctcttcgttc------tcttcgcgttttcgtgttcttcctccatagctagacttcaaagcctcactaaccgtttcattcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTTTGGCATTGTCCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC
|| ||||| | | | | | | || || | || || | ||| | | ||| | | | ||| |||||||| |||||||| | |||| || ||||||||||| |||||||||||| |||| |||||||||| | ||||| || |||| ||||| ||
taggtctatgcattatgaacaagacacaaaaaataaaagagaggaagaaaaaagccaccttttatattgtttagagctaaattggtggttg---ttactacagGGAGATGATTCAGCACAGACCCTACAATCATAAGGTGGACGTGTACAGCTTTGGCGTTGTTTTGTGGGAGCTTGTGACAGGCCTGTTACCCTTCCAAAATMapped 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|169033117|gb|FE441449.1|FE441449EST: CAGACCGAGGGGATGACGCCCGAGACCGGGACGTATCGCTGGATGGCACC AGAGATGATCCAGCACAGGCTTTACACGCACAAGGTGGACGTTTACAGCTT
genomic: CAGACCGAGGGGATGACGCCCGAGACCGGGACGTATCGCTGGATGGCACCgtaagcgcat ... ttcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTT
EST:
gi|169040652|gb|FE449783.1|FE449783EST: CAGACCGAGGGGATGACGCCCGAGACCGGGACGTATCGCTGGATGGCACC AGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTT
genomic: CAGACCGAGGGGATGACGCCCGAGACCGGGACGTATCGCTGGATGGCACCgtaagcgcat ... ttcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTT
EST:
gi|169033116|gb|FE441448.1|FE441448EST: CAGACCGAGGGGATGACGCCCGAGACCGGGACGTATCGCTGGATGGCACC AGAGATGATCCAGCACAGGCTTTACACGCACAAGGTGGACGTTTACAGCTT
genomic: CAGACCGAGGGGATGACGCCCGAGACCGGGACGTATCGCTGGATGGCACCgtaagcgcat ... ttcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTT
EST:
gi|169051311|gb|FE457635.1|FE457635EST: CAGACCGAGGGGATGACGCCCGAGACCGGGACGTATCGCTGGATGGCACC AGAGATGATCCAGCACAGGCTTTACACGCACAAGGTGGACGTTTACAGCTT
genomic: CAGACCGAGGGGATGACGCCCGAGACCGGGACGTATCGCTGGATGGCACCgtaagcgcat ... ttcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTT
EST:
gi|169030867|gb|FE440306.1|FE440306EST: CAGACCGAGGGGATGACGCCCGAGACCGGGACGTATCGCTGGATGGCACC AGAGATGATCCAGCACAGGCTTTACACGCACAAGGTGGACGTTTACAGCTT
genomic: CAGACCGAGGGGATGACGCCCGAGACCGGGACGTATCGCTGGATGGCACCgtaagcgcat ... ttcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTT
EST:
gi|169057240|gb|FE464192.1|FE464192EST: CAGACCGAGGGGATGACGCCCGAGACCGGGACGTATCGCTGGATGGCACC AGAGATGATCCAGCACAGGCTTTACACGCACAAGGTGGACGTTTACAGCTT
genomic: CAGACCGAGGGGATGACGCCCGAGACCGGGACGTATCGCTGGATGGCACCgtaagcgcat ... ttcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTT
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:
34CCGATAAGTCGATCAAGATTGCCGACTTTGGCGTGGCCAGGATCGAGGTCCAGACCGAGGGGATGACGCCCGAGACCGGGACGTATCGCTGGATGGCACCgtaagcgcat ... ttcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTTTGGCATTGTCCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttcttcctccatagctagacttcaaagcctcactaaccgtttcattcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTTTGGCATTGTCCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC
cactaac putative branch site (score: 34)
tttcattc putative PPT
tttcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcgcatttctctcttcgttctcttcgcgttttcgtgttcttcctccatagctagacttcaaagcctcactaaccgtttcattcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTTTGGCATTGTCCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA