Sequence
atgc intronic sequence ATGC exonic sequence...atgctactttttgctcattcgtgttgaagggggttatgcttgtgatggaaagatcattctcattcattcaatagctgagagcaggtgattttcattgcagGCAGATATATGGTCATTGGGGATCACCGCTATTGAGATGGCAAAAGGGGAGCCACCTTACGCAGATCTGCATCCTATGCGTGTTCTTTTTCTTATTCCTA
Basic information
species | Physcomitrella patens |
transcript | PP1S59_173V6.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S59_173V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 8
atgctactttttgctcattcgtgttgaagggggttatgcttgtgatggaaagatcatt-ctcattcattcaatagctgagagcaggtgattttcattgcagGCAGATATATGGTCATTGGGGATCACCGCTATTGAGATGGCAAAAGGGGAGCCACCTTACGCAGATCTGCATCCTATGCGTGTTCTTTTTCTTATTCCTA
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----------------------gtagctgtgcgtttttctt----taaacagtttgctgcttactgaactttttacccaagtc---tgtgtcctgatgcagGCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAACCCCCTTTGGCAGATATCCATCCCATGAGAGTTCTTTTCATGATACCTC
upper sequence: PP1S59_173V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 8
------------------------------atgctactttttgctcattcgtgttgaagggggttatgcttgtgatggaaagatcattctcattcattcaatagctgagagcaggtgattttcattgcagGCAGATATATGGTCATTGGGGATCACCGCTATTGAGATGGCAAAAGGGGAGCCACCTTACGCAGATCTGCATCCTATGCGTGTTCTTTTTCTTATTCCTA
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gttgtaatatatttagtctaaatctcttttgttatgtttctctttggttctgtttttccacctttattttcagtttgtgatagtcattggattttttagaatcatcactggagtattctgttt-ttgcagGCAGATATCTGGTCTCTGGGAATCACTGCAATTGAGATGGCAAAGGGGGAGCCGCCACTTGCTGATCTTCACCCAATGAGAGTGCTTTTCATTATACCCC
upper sequence: PP1S59_173V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 9
---------------------------------atgctactttttgctcattcgtgttgaagggggttatgcttgtgatggaaagatcattctcattcattcaatagctgagagcaggtgattt-tcattgcagGCAGATATATGGTCATTGGGGATCACCGCTATTGAGATGGCAAAAGGGGAGCCACCTTACGCAGATCTGCATCCTATGCGTGTTCTTTTTCTTATTCCTA
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gttgtaatatatttagtctaaatctcttttgttatgtttctctttggttctgttttttcac-----ctttatttttagtttgttagtcattgtttttcttagaatcatcactgg--agtaatctgtttttgcagGCAGATATCTGGTCTCTGGGAATCACTGCAATTGAGATGGCAAAGGGGGAGCCTCCACTTGCTGATCTTCACCCAATGAGAGTGCTTTTCATTATACCCC
upper sequence: PP1S59_173V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA12G27300.1 (Glycine max), 3'ss of exon 9
----------------------------atgctactttttgctcattcgtgttgaagggggttatgcttgtgatggaaagatcattctcattcattcaatagc-tgagagcaggtgattttcat--------tgcagGCAGATATATGGTCATTGGGGATCACCGCTATTGAGATGGCAAAAGGGGAGCCACCTTACGCAGATCTGCATCCTATGCGTGTTCTTTTTCTTATTCCTA
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gttatcttatagttactactcaaatcatttattatgctttctgagttcatcctaacatatttcttttcatcctctgttcctttattgtttttgtttttatcccctaagaatcatcactctgtatcttgtttatacagGCAGATATCTGGTCTCTGGGCATTACTGCGATTGAGATGGCAAAAGGGGAGCCTCCACTTGCTGATCTTCATCCAATGAGAGTGCTTTTCATCATACCCC
upper sequence: PP1S59_173V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA06G36130.3 (Glycine max), 3'ss of exon 8
---------------------------atgctactttttgctcattcgtgttgaagggggttatgcttgtgatggaaagatcattctcatt-cattcaatagctgagagcaggtgattttcat--------tgcagGCAGATATATGGTCATTGGGGATCACCGCTATTGAGATGGCAAAAGGGGAGCCACCTTACGCAGATCTGCATCCTATGCGTGTTCTTTTTCTTATTCCTA
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gtatttttatagttactacaaaaatcatttatgttttctttgagttcatgctaacatgtttctttttattctctgttcctttattgtttttgtttttatcccctaagaatcatcactctgtatcttgtttatacagGCAGATATATGGTCTCTGGGCATTACTGCAATAGAGATGGCAAAAGGGGAGCCTCCACTTGCTGATCTTCATCCAATGAGAGTGCTTTTCATCATACCCC
upper sequence: PP1S59_173V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv19s0014g02310.t01 (Vitis vinifera), 3'ss of exon 9
-atgctactttttgctcattcgtgttgaagggggttatgcttgtgatggaaagatcattctcattcattcaatagctgagagcaggtgattttcattgcagGCAGATATATGGTCATTGGGGATCACCGCTATTGAGATGGCAAAAGGGGAGCCACCTTACGCAGATCTGCATCCTATGCGTGTTCTTTTTCTTATTCCTA
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tgaggtggtcagtatttgtgtttctccttttttgccatgttttgtccatttggtgcttcctcccacttctgatattattgggcca-tgaacaatgatgcagGCGGATATTTGGTCTCTGGGAATAACTGCAATTGAGATGGCAAAAGGGGAGCCTCCACTTGCAGATCTCCATCCAATGAGAGTGCTTTTTATAATACCTCMapped 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|100383755|gb|BY969284.1|BY969284EST: GGATGGCGCCAGAGGTCATACAGAACTCTGGAGATGGCTACAATGAGAAG GCAGATATATGGTCATTGGGGATCACCGCTATTGAGATGGCAAAAGGGGAG
genomic: GGATGGCGCCAGAGGTCATACAGAACTCTGGAGATGGCTACAATGAGAAGgtaatcggaa ... ttcattgcagGCAGATATATGGTCATTGGGGATCACCGCTATTGAGATGGCAAAAGGGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggaaagatcattctcattcattcaatagctgagagcaggtgattttcattgcagGCAGATATATGGTCATTGGGGATCACCGCTATTGAGATGGCAAAAGGGGAGCCACCTTACGCAGATCTGCATCCTATGCGTGTTCTTTTTCTTATTCCTA
ttttcatt CT-rich tract
attttcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgctactttttgctcattcgtgttgaagggggttatgcttgtgatggaaagatcattctcattcattcaatagctgagagcaggtgattttcattgcagGCAGATATATGGTCATTGGGGATCACCGCTATTGAGATGGCAAAAGGGGAGCCACCTTACGCAGATCTGCATCCTATGCGTGTTCTTTTTCTTATTCCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT