Sequence
atgc intronic sequence ATGC exonic sequence...taattttcgcaggtttcaggatcccctagctctggacttatggccgtgcacaaagctgataatcctttgctgaaactcttcacgtgcgtgatggtgacagGGATTCAGGAAGGTGGTGCCCGACCGGTGGGAGTTCGCGAACGATTTTTTCCGACGAGGAGAGCGGCACCTCCTTTGCGAGATATACAGGCGGAAGGCAT
Basic information
species | Physcomitrella patens |
transcript | PP1S19_153V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S19_153V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os09g28200.1 (Oryza sativa), 3'ss of exon 1
taattttcgcaggtttcaggatcccctagctctggacttatggccgtgcacaaagctgataatcctttgctgaaactcttcacgtgcgtgatggtgacagGGATTCAGGAAGGTGGTGCCCGACCGGTGGGAGTTCGCGAACGATTTTTTCCGACGAGGAGAGCGGCACCTCCTTTGCGAGATATACAGGCGGAAGGCAT
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----gtaagcaaagcgccatgccgccaccttctgtagttctgttctctcgtgcgttt--tgatgcgt----gtaagtaacgacgt-cgttgcaatg-cagGGGTTCAGGAAGGTCGTGCCGGAGAGGTGGGAGTTCGCGAACGAGTTCTTCAGGAAGGGGGAGAAGCAGCTGCTCACCGAGATCCACCGCAGGAAGACGTMapped 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|67719956|gb|BJ970215.1|BJ970215EST: ATTTCAAACACAACAACTTTTCCAGCTTTGTGCGACAACTAAATACTTAT GGATTCAGGAAGGTGGTGCCCGACCGGTGGGAGTTCGCGAACGATTTTTTC
genomic: ATTTCAAACACAACAACTTTTCCAGCTTTGTGCGACAACTAAATACTTATgtaagctccg ... atggtgacagGGATTCAGGAAGGTGGTGCCCGACCGGTGGGAGTTCGCGAACGATTTTTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgcacaaagctgataatcctttgctgaaactcttcacgtgcgtgatggtgacagGGATTCAGGAAGGTGGTGCCCGACCGGTGGGAGTTCGCGAACGATTTTTTCCGACGAGGAGAGCGGCACCTCCTTTGCGAGATATACAGGCGGAAGGCAT
agctgat putative branch site (score: 4)
tgataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taattttcgcaggtttcaggatcccctagctctggacttatggccgtgcacaaagctgataatcctttgctgaaactcttcacgtgcgtgatggtgacagGGATTCAGGAAGGTGGTGCCCGACCGGTGGGAGTTCGCGAACGATTTTTTCCGACGAGGAGAGCGGCACCTCCTTTGCGAGATATACAGGCGGAAGGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - -gtgcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacgtgc