Sequence
atgc intronic sequence ATGC exonic sequencegtaagatcatatcccatccatcaccagttttggtttttagttcttaaattttttgctttctttatatgatcatttggatgacttccactgagctctgatatactcgcgtgataaacagACTGATAAAGCCTCGATGCTCGACGAAATCATCGACTACGTAAAGTTTTTGCAGCTCCAAGTCAAG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ12627 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ12627 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os06g08500.1 (Oryza sativa), 3'ss of exon 3
gtaagatcatatcccatccatcaccagttttggtttttagttcttaaattttttgctttctttatatgatcatttggatgacttccactgagctctgatatactcgcgtgataaacagACTGATAAAGCCTCGATGCTCGACGAAATCATCGACTACGTAAAGTTTTTGCAGCTCCAAGTCAAG
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--------tgggcgcattcgtgcccaattttg--tcatcgtt------tttcttgacatcttgatgaagaaaatgaagtga-ttgaatggagttctttgat-ttgattttgcttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG
upper sequence: EFJ12627 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G067654_T01 (Zea mays), 3'ss of exon 4
gtaagatcatatcccatcca--tcaccag-----ttttggtttttagttcttaaattttttgctttctttatatgatcatttggatgacttc-cactg-agctctgatatactcgcgtga---taaacagACTGATAAAGCCTCGATGCTCGACGAAATCATCGACTACGTAAAGTTTTTGCAGCTCCAAGTCAAG
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gtcgg--catcccccctctagctagctagctcctttctcttctctctcgctcgcgtcgtcaacaatcaacagacaa-cactgaaatggcgacgtggtgtgggtcggtcgtcgttgtttgtggttttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAGGTTCTTGCAGCTCCAAGTCAAG
upper sequence: EFJ12627 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G350165_T01 (Zea mays), 3'ss of exon 4
gtaagatcatatcccatccatcaccagttttggtttttagttcttaaattttttgctttctttatatgatcatttggatgacttccactgagctctgatatactcgcgtgataaacagACTGATAAAGCCTCGATGCTCGACGAAATCATCGACTACGTAAAGTTTTTGCAGCTCCAAGTCAAG
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----------------cttgtcgt-aatgtcgtccaccctctatcctccttttcgttcttcgcgcttgacttcctcgccgacgactgatccatcatctcaatgtcttgt-atctgcagACGGACAAGGCGTCGATGCTGGACGAGATCGTCGACTACGTCAAGTTCCTTCAGCTCCAAGTCAAG
upper sequence: EFJ12627 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S173_83V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaagatcatatcccatccatcaccagttttggtttttagttcttaaattttttgctttctttatatgatcatttggatgacttccactgagctctgatatactcgcgtgataaacagACTGATAAAGCCTCGATGCTCGACGAAATCATCGACTACGTAAAGTTTTTGCAGCTCCAAGTCAAG
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--------------gaaacttcgtgtatttttttcatctactttca---cttgggcttattttaaaatctaattagaagaaatgatccaatcctcttactgctgtctgtgg-atacagACGGATAAGGCGTCGATGCTGGATGAAATCATCGATTACGTCAAGTTCCTGCAACTCCAAGTAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgatcatttggatgacttccactgagctctgatatactcgcgtgataaacagACTGATAAAGCCTCGATGCTCGACGAAATCATCGACTACGTAAAGTTTTTGCAGCTCCAAGTCAAG
ctctgat putative branch site (score: 4)
atcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatcatatcccatccatcaccagttttggtttttagttcttaaattttttgctttctttatatgatcatttggatgacttccactgagctctgatatactcgcgtgataaacagACTGATAAAGCCTCGATGCTCGACGAAATCATCGACTACGTAAAGTTTTTGCAGCTCCAAGTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC