Sequence
atgc intronic sequence ATGC exonic sequencegtaattttcttctgcattcgtcttagatcttttcattattgagtattcccgtcttaacattgattactcttcaaaggtgcatcctgttctgagtcttgctgatatggcacttgtcgtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGT
Basic information
species | Physcomitrella patens |
transcript | PP1S47_46V6.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G074037_T01 (Zea mays), 3'ss of exon 6
gtaattttcttctgcattcgtcttagatcttttcattattgagtattcccgtcttaacattgattactcttcaaaggtgcatcctgttctgagtcttgctgatatggcacttgtcgtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGT
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-------acacccgtggcccgtgcataatttcttttaattgaagtgcataatccgtgtatatgtcattgctataaaatgt----tgtctttggttttat----------cttgttgcct----agCCATGCATCATTTTCATGGATGAAATTGATGCCATTGGTGGCCGAAGATTTAGTGAGGGCACAAGTGCAGATCGTGAGATTCAGAGGACATTGATGGAGC
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA06G03230.1 (Glycine max), 3'ss of exon 6
gtaattttcttctgcattcgtcttagatcttttcattattgagtattcccgtcttaacattgattactcttcaaaggtgcatcctgttctgagtct-tgctgatatggcacttgtcgtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGT
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--------------------------------------gtgag-atgcttgtgtgaaattgtcttcctataggtttacacatactaatttaaagatgttctaaatctatacttttcttgatt--agCCGTGCATCATTTTTATGGATGAGATCGATGCCATTGGAGGTCGCCGTTTCAGTGAGGGAACAAGTGCAGATCGTGAGATTCAGAGAACGCTAATGGAGC
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA04G03180.1 (Glycine max), 3'ss of exon 6
gtaattttcttctgcattcgtcttagatcttttcattattgagtattcccgtcttaacattgatt-actcttcaaaggtgcatcctgttctgagtcttgctgatatggcacttgtcgtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGT
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-----------------------------gtgagataattgtgtgaaattgtcttcctataggtttacacatactaattgaaagatgttctaaatct-----atacattacttgat-------tagCCTTGCATCATTTTTATGGATGAGATCGATGCCATTGGAGGTCGCCGTTTCAGTGAGGGAACAAGTGCAGATCGTGAGATTCAGAGAACGCTAATGGAGC
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA14G07750.1 (Glycine max), 3'ss of exon 6
gtaattttcttctgcattcgtcttagatcttttcattattgagtattcccgtcttaacattgatt-actcttcaaaggtgcatcctgttctgagtcttgctgatatggcacttgtcgtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGT
| |||| | | || || || | | ||| | || ||||||||||| | | | |||| | |||| ||||| || |||||||||||||| ||||| ||||| || ||| | || || || || |||||||| ||||| |||||||| | ||||| |||||||
----------------------------------------gtagattcttgaatgaagtttctttcatatattaaaatggaatatggttctgagtctc------------cattttgtttgttaagCCTTGCATCATTTTTATGGATGAGATCGATGCCATTGGTGGTCGTCGTTTCAGTGAGGGAACAAGTGCTGATCGTGAGATTCAGAGAACACTAATGGAGT
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv03s0038g04350.t01 (Vitis vinifera), 3'ss of exon 6
gtaattttcttctgcattcgtcttagatcttttcattattgagtattcccgtcttaacattgattactcttcaaaggtgcatcctgttctga-gtcttgctgatatggcacttgtcgtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGT
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--------------------------------------gtaagtgtttgaatt---gcatgggattttttcgatttgtgaaatctttgccaatgatattctaat-tactgttttttgcttgtcaagCCCTGTATCATTTTTATGGATGAGATTGATGCCATTGGTGGGCGTCGTTTCAGCGAGGGAACAAGTGCTGATCGTGAAATTCAGAGAACACTCATGGAGTMapped 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|18338881|gb|BJ170907.1|BJ170907EST: AAAGTGCGAGACTCATTAGAGAGATGTTTAGTTATGCTCGCGACCATCAA CCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTT
genomic: AAAGTGCGAGACTCATTAGAGAGATGTTTAGTTATGCTCGCGACCATCAAgtaattttct ... gtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaaggtgcatcctgttctgagtcttgctgatatggcacttgtcgtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGT
tgctgat putative branch site (score: 3)
tcgttttt putative PPT
ttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattttcttctgcattcgtcttagatcttttcattattgagtattcccgtcttaacattgattactcttcaaaggtgcatcctgttctgagtcttgctgatatggcacttgtcgtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
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