Sequence
atgc intronic sequence ATGC exonic sequence...cattcggtcactcctttttgctttgcacaatttaagtagaaacaatccaacaatctggccatgtcctttcactttctcgttatgaaatgtttttctatagAGCAATCCCGAAATTGTGAAGCGATGGAGTAATGAAGTTCAAGAGGCTGTTCAGTCCAAGGCACCACTTGTTCAGTTCCATGGTTTGGCATTGCTTCATC
Basic information
species | Physcomitrella patens |
transcript | PP1S41_154V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S41_154V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 5
------cattcggtcactcctttttgctttgcacaatttaagtagaaacaatccaacaatctggccatgtcctt-tcactttctcgttatgaaatgtttttctatagAGCAATCCCGAAATTGTGAAGCGATGGAGTAATGAAGTTCAAGAGGCTGTTCAGTCCAAGGCACCACTTGTTCAGTTCCATGGTTTGGCATTGCTTCATC
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gtatgtcctgcagtta-tattttgtgctccagttggatatattgttactagttggtgcagctatagatatttttattatgttttccacatgtttgtattattggcagACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACC
upper sequence: PP1S41_154V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 5
---cattcggtcactcctttttgctttgcacaatttaagtagaaacaatccaacaatctggccatgtcctttcactttctcgttatgaaatgtttttctatagAGCAATCCCGAAATTGTGAAGCGATGGAGTAATGAAGTTCAAGAGGCTGTTCAGTCCAAGGCACCACTTGTTCAGTTCCATGGTTTGGCATTGCTTCATC
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gtatgtcctgt-gctccacttggatatattgttactagtttgtggcagc-------tttagttcttttttattatgttttccacatgtttgtactattggcagACAAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAGTTTCATGCCCTTGCTCTCCTTCACCMapped 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|100451181|gb|CJ974637.1|CJ974637EST: ATCCTGTTGTTTCGAGCGCTGCACTAGTCAGCGGTATCCATCTACTTCAG AGCAATCCCGAAATTGTGANGCGATGGAGTAATGAAGTNCAAGAGNCTGTN
genomic: ATCCTGTTGTTTCGAGCGCTGCACTAGTCAGCGGTATCCATCTACTTCAGgtagtatgtt ... ttttctatagAGCAATCCCGAAATTGTGAAGCGATGGAGTAATGAAGTTCAAGAGGCTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccaacaatctggccatgtcctttcactttctcgttatgaaatgtttttctatagAGCAATCCCGAAATTGTGAAGCGATGGAGTAATGAAGTTCAAGAGGCTGTTCAGTCCAAGGCACCACTTGTTCAGTTCCATGGTTTGGCATTGCTTCATC
tgtttttct CT-rich tract
ttatgaaatgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattcggtcactcctttttgctttgcacaatttaagtagaaacaatccaacaatctggccatgtcctttcactttctcgttatgaaatgtttttctatagAGCAATCCCGAAATTGTGAAGCGATGGAGTAATGAAGTTCAAGAGGCTGTTCAGTCCAAGGCACCACTTGTTCAGTTCCATGGTTTGGCATTGCTTCATC
- - - - - - - - - - - ttgcaca