Sequence
atgc intronic sequence ATGC exonic sequenceCGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatgcctcgcatcaatcttttcgtctttctattccaattcgatgtgggttttcgcaagattttgatgtggattcttggcttcttctgctag
Basic information
species | Selaginella moellendorffii |
transcript | EFJ29711 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ29711 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os03g04750.1 (Oryza sativa), 5'ss of exon 1
CGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtat-----gcctcgcatcaatcttttcgtctttctattccaattcgatgtgggttttcgcaagattttgatgtggattcttggcttcttctgctag---
||| | |||||||||||||||||||| |||||||||||||||||||| || ||||| |||||||||||||| |||| |||||||| ||||||||||||| || ||| | | | || | | || | | | | | || | | | | | | | | | ||| | |
CGCCGTGCACAAGGGCATGCCGCACAAGTTCTACCACGGCCGCACCGGCCGCGTCTGGAACGTCACCAAGCGCGCCATCGGCGTCGAGATCAACAAGCAGgtataatccgctccgctccggccatagcggcatcctttcctcttcctccctcttttcttctcaacaggcggtagatttggtagatctgtgctgttggctc
upper sequence: EFJ29711 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os10g32820.1 (Oryza sativa), 5'ss of exon 1
CGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatgcctcgca----tcaatcttttcgtcttt--ctattccaattcgatgtgggttttcgcaagattttgatgtggattcttggcttcttctgctag---
||| | |||||||| ||||||||||| |||||||||||||||||||| || ||||| |||||||||||||| |||| |||||||| ||||||||||||| | | | ||| | || | | || || | | | | | | | | | | | | ||||| || | | | |
CGCCGTGCACAAGGGGATGCCGCACAAGTTCTACCACGGCCGCACCGGCCGCGTCTGGAACGTCACCAAGCGCGCCATCGGCGTCGAGATCAACAAGCAGgtataacccccgatccccaaacaccccggcggcggcgccgcctctttgtcatagatctgtggttg-tgtcgcttaagtgacttggtgtcatgtttttgccc
upper sequence: EFJ29711 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G089421_T01 (Zea mays), 5'ss of exon 1
CGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatgcctc--gcatca---atcttttcgtctttctattccaattcgatgtgggttttcgcaagattttgatgtggattcttggcttcttctgc-tag---
||| | |||||||||||||||||||| ||||||||||||||||||||| || ||||| |||||||||||||| |||| |||||||| ||||||||||||| ||| ||| || | | | ||| ||| |||| || | ||||| | | || || ||| || | ||| |||
CGCCGTGCACAAGGGCATGCCGCACAAGTTCTACCACGGCCGCACCGGGAGCGTCTGGAACGTCACCAAGCGCGCCATCGGCGTCGAGATCAACAAGCAGgtataactcccgcaccagctaccatgctgtcgttc-gttccgtatcagcattcgttttgttagatctatgctgctgatgctaatacacggatgcataggta
upper sequence: EFJ29711 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G026216_T01 (Zea mays), 5'ss of exon 1
CGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatgcctcgcatcaatcttttcgt---ctttctattcca--attcgatgtgggttttcgcaagattttg-atgtggattcttggcttcttctgctag--
||| |||||||||| ||||||||||| |||||||||||||||||||| || ||||| |||||||||||||| |||| |||||||| ||||||||||||| || | | ||||||| || || | | | | || | | || |||| || | | || | ||
CGCCGTCCACAAGGGGATGCCGCACAAGTTCTACCACGGCCGCACCGGTCGCGTCTGGAACGTCACCAAGCGCGCCATCGGCGTCGAGATAAACAAGCAGgtataccacacggatcccttttcgctagctcgctgataggttgctgggcgcaggcagttgaaatcgtttgtgcacggcgcttacgtttagtgcgcggacg
upper sequence: EFJ29711 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G149257_T01 (Zea mays), 5'ss of exon 1
CGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatgcc--tcgcatcaatct------tttcgtctttctattccaattcgatgtgggttttcgcaagattt--tgatgtggattcttggcttcttctgctag
||| | |||||||||||||||||||| |||||||||||||||||||| || ||||| |||||||||||||| |||| || ||||| ||||||||||||| | |||| || | | | ||| ||| | | || || | ||||| | | | | || || | || |||| | | || |
CGCCGTGCACAAGGGCATGCCGCACAAGTTCTACCACGGCCGCACCGGTCGCGTCTGGAACGTCACCAAGCGCGCCATCGGCGTTGAGATCAACAAGCAGgtataacgcccgcaccagcataccctgtgttgtcattcgttccgtatgcgccgccggtttgctagatgtgtgctgctgctggttgatggcaa-tacagcga-
upper sequence: EFJ29711 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA19G39240.1 (Glycine max), 5'ss of exon 1
CGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgt---atgcctcgcatcaatcttt---tcgtctttctattccaattcgatgtgggttttcgcaagattt-tgatgtggattcttggcttcttctgctag-
|| | |||||||| ||||| |||||||||||||| ||||||||||| || |||||||||||||| || || || || ||||| | ||||||||||| | | | | || | | | | |||| | | | | | | | | | | ||| || | ||| | |||| ||
TGCCGTTCACAAGGGAATGCCCCACAAATTCTACCATGGCCGCACCGGACGCGTCTGGAATGTCACCAAACGTGCTGTTGGCGTCGAAGTCAACAAGCAGgtctcacactcttccttaaccctagcaccacccttctttccttttctgcttttcgatctgttgtgttttctgtttcttattgtgatattctcgtgtcgaa
upper sequence: EFJ29711 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA03G36560.1 (Glycine max), 5'ss of exon 1
CGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatgcctcgca-tcaatcttttcgtctttctattccaatt-cgatgtgggttttcgcaagattttgatgtggattcttggcttcttctgctag-----------
||| |||||||||| ||||| ||||| |||||||| ||||||||||| || |||||||||||||| || || || || ||||| | ||||||||||| |||||| || | || | | | || | || | | | || ||| ||||| | || || || | | | |||
CGCCGTCCACAAGGGAATGCCACACAAGTTCTACCATGGCCGCACCGGTCGCGTCTGGAATGTCACCAAACGTGCTGTTGGGGTCGAAGTCAACAAGCAGgt----ctcgcactctcttccttaaccctaacactctatttacttttctgcttctcgatctgttttgttatgtctttttta-tcgtgatactatcgcttccaatt
upper sequence: EFJ29711 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AT1G09690.1 (Arabidopsis thaliana), 5'ss of exon 1
CGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatgcc--tcgcatcaatcttttcgtctttc---tattccaattcgatgtgggttttcgcaagattttgatgtggattcttggcttcttctgctag----
|||||||||||||| ||||| ||||| ||||||||||| || || || | | ||||| ||||| || ||||| ||||| || || | ||||| ||||| || | | | |||| ||| |||| | | |||| | | | ||| | | | || |||||| ||| | || |
TGCGATCCACAAGGGTATGCCTCACAAGTTCTACCACGGTCGTACTGGTCGTATCTGGAACGTCACTAAACGCGCCGTCGGTGTTGAAGTCAACAAACAGgtctgatgaactctcctatctcttcagcttttgtgtcattgaattaggatttgagcttcttagtgtgct-atttggattgttgatctattgctttgatgta
upper sequence: EFJ29711 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv08s0007g06890.t01 (Vitis vinifera), 5'ss of exon 1
CGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatgcctcgcatcaatcttttcgtctttctattccaat-tcgatgtgggttttcgcaagattttgatgtggattcttggcttcttctgctag---------
||| |||||||||||||||| ||||| |||||||| |||||||| || || ||||| |||||||||||||| |||| || || | ||||||||||| | | | |||| | ||| ||| | | | | |||| || || || || | || || | || | |
CGCCGTCCACAAGGGCATGCCCCACAAGTTCTACCATGGCCGCACTGGTAAGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctctcctctac--atctctatctctctctgatgtgttgttgttgtgttttgatcgtagtttatgggtttaatgttttgtttgtgtgaaaatggtggttga
upper sequence: EFJ29711 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv08s0007g07010.t01 (Vitis vinifera), 5'ss of exon 1
CGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatgcctcgcat-----caatcttttcgtctt--tctattccaattcgatgtgggttttcgcaagattttgatgtggattcttggcttcttctgctag-
||| ||||||||||||||||| ||||| |||||||| |||||||| || || ||||| || || |||||||| |||| ||||| | ||||||||||||| | || | | | | | || | | |||||| || || | | || | | || || | || | |||| || | || |
CGCCATCCACAAGGGCATGCCCCACAAGTTCTACCATGGCCGCACTGGTAAGGTCTGGAACGTTACTAAGCGCGCCATCGGCGTCGAAGTAAACAAGCAGgtatccttctctttctgcccgtgtcttgattgtaatctatttgtatggtattttgtttgtgtggaaatggtgttttgattgattgggttttcttgatttt
upper sequence: EFJ29711 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv01s0150g00520.t01 (Vitis vinifera), 5'ss of exon 1
CGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatgcctcgcatcaatcttttcgtctttctattccaattcgatgtgggttttcgcaagattttga-tgtggattcttggcttcttctgctag---------
||| || |||||||||||||| ||||| ||||| || ||||||||||| || ||||| ||||||||||| || | || || || | ||||| |||| || ||| | ||| || | | |||| || | | | | || || ||| ||| | ||| | || | ||
CGCCATTCACAAGGGCATGCCCCACAAGTTCTATCATGGCCGCACCGGCAAGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAGgcatctctcttcttctccttgtc-tttctctactctgctgcatcattc-tattatcattattatgaatccagatctcttcaacattttcatatttccaattc
upper sequence: EFJ29711 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S298_23V6.1 (Physcomitrella patens), 5'ss of exon 1
CGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatg----cctcgcatcaatcttttcgtctttctattccaattcgatgtgg-------gttttcgcaagattttgatgtggattcttggcttcttctgctag
|| |||||||||| ||||| ||||| ||||||||||| |||||||| | || |||||||||||||||||||| || || |||| ||||||||||||||| | | | ||| | |||| | || | |||| || | || | |||| | | || | ||
AGCCGTCCACAAGGGAATGCCCCACAAGTTCTACCACGGGCGCACCGGTATCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgttttttttacgatccaacggcaattcttgtggtttttgttgtgccccttgtgtccttacatcagacgcatgtagcattctgtttctgtccat---
upper sequence: EFJ29711 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S107_181V6.1 (Physcomitrella patens), 5'ss of exon 1
CGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatgcctcgcatcaatcttttcgtctttctattccaattcgatgtgggttttcgc----aagattttgat--gtggat---tcttggcttcttctgctag
|| |||||||||| ||||| ||||| ||||||||||| |||||||| | || ||||| |||||||||||||| || || |||| |||||||||||||||||| | | || |||| || || | | || || || | | | | || ||| | |||| | |||| || || |
TGCTGTCCACAAGGGTATGCCTCACAAGTTCTACCACGGACGCACCGGCATCGTCTGGAACGTCACCAAGCGCGCCGTTGGTGTCGTGATGAACAAGCAGgtatggtctctttgtacctcttcggctgtcgtctacttttggagatgtctgtctggcttaatgactttcgtctgtgggtgcgtcttcgccactattctcg-
upper sequence: EFJ29711 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S1_780V6.1 (Physcomitrella patens), 5'ss of exon 1
CGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatgcctcgcatcaatcttttcgtctttctattccaattcg-------atgtgggttttcgcaagat--tttgatgtggattcttggcttcttctgctag
|| |||||||||| ||||| ||||| ||||||||||| |||||||| | || ||||| ||||||||||| || ||||| |||| |||||||||||||||||| | | | | | | | | | || || || | | | | | | || | | | | | || |||||| |||
AGCCGTCCACAAGGGTATGCCTCACAAGTTCTACCACGGGCGCACCGGCATCGTCTGGAACGTCACCAAGCGTGCCGTCGGTGTCGTGATGAACAAGCAGgtatgattgaccttctccctccctcccccgaagccgaagccgcctggtcgtgggagctcccccttcctgcttcgttctagggtttttccttctttggctg-
upper sequence: EFJ29711 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S91_107V6.1 (Physcomitrella patens), 5'ss of exon 1
CGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatg--cctcgcatcaatcttttcgtctttctattccaattcgatgtgggttttcgcaagattttgatgtggattcttggcttcttctgctag----------
|| | |||||||| ||||| ||||| ||||||||||||||||| || |||| ||||| |||||||||||||| ||||| || | |||||||||||||||| | ||| | | | ||| | ||| | | ||| | || |||| | || | || || || | ||| | ||
AGCCGTTCACAAGGGTATGCCCCACAAGTTCTACCACGGCCGCACTGGAATTGTCTGGAACGTCACCAAGCGCGCCGTCGGCGTTGTGATGAACAAGCAGgtacggttctctcgctatccgttttttttttttggtggaatccagcttg---tttcagtcggttccggcgttccttgttt-cagcttacaccagaatattgtgaMapped 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|169110919|gb|FE514212.1|FE514212EST: TTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAG GTGGGGAACAGGATCATCAAGAAGAGGCTACACGTCCGGATCGAGCACGTC
genomic: TTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatgcctcg ... cttctgctagGTGGGGAACAGGATCATCAAGAAGAGGCTACACGTCCGGATCGAGCACGTC
EST:
gi|169069141|gb|FE477794.1|FE477794EST: TTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAG GTGGGGAACAGGATCATCAAGAAGAGGCTACACGTCCGGATCGAGCACGTC
genomic: TTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatgcctcg ... cttctgctagGTGGGGAACAGGATCATCAAGAAGAGGCTACACGTCCGGATCGAGCACGTC
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:
109CGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatgcctcg ... cttctgctagGTGGGGAACAGGATCATCAAGAAGAGGCTACACGTCCGGATCGAGCACGTCAAGCCCTCGCGCTGCCGGGAGGATTTCCTCAAGAGAATCAAGAGCAGTG
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatgcctcgcatcaatcttttcgtctttctattccaattcgatgtgggttttcgcaagattttgatgtggattcttggcttcttctgctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG