Sequence
atgc intronic sequence ATGC exonic sequence...acattgtacaaatcctcaaagcatatgctaaatcttttgtgcatagttgtagtatttaagttcagtcttgtatattgactttgtatgcttaaaactgcagGTTATATCAGGGAAGCTCTATGCCGGTCCTGAGGTGGACGTCTGGAGCTGTGGCGTTATTCTGTATGCTCTCTTGTGTGGCTCGTTGCCCTTCGACGACG
Basic information
species | Physcomitrella patens |
transcript | PP1S7_365V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S7_365V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G077278_T01 (Zea mays), 3'ss of exon 4
acattgtacaaatcctcaaagcatatgctaaatcttttgtgcatagttgtagtatttaagttca-gtcttgt-atattgactttgtatgcttaaaactgcagGTTATATCAGGGAAGCTCTATGCCGGTCCTGAGGTGGACGTCTGGAGCTGTGGCGTTATTCTGTATGCTCTCTTGTGTGGCTCGTTGCCCTTCGACGACG
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---------gtatcatcta-gcataatttacaattagcgtccttcatggttgcatttacatatataacttgccatgacacgtttctgt-cttattttcttagGTCATATCTGGTAAACTATATGCTGGTCCTGAAGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATG
upper sequence: PP1S7_365V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 4
----acattgtacaaatcctcaaag-catatgctaaatct-tttgtgcatagttgtagtattt--aagttcagtcttgtatattgactttgtatgcttaaaa---ctgcagGTTATATCAGGGAAGCTCTATGCCGGTCCTGAGGTGGACGTCTGGAGCTGTGGCGTTATTCTGTATGCTCTCTTGTGTGGCTCGTTGCCCTTCGACGACG
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gtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG
upper sequence: PP1S7_365V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EDO99409 (Chlamydomonas reinhardtii), 3'ss of exon 5
--acattgtacaaatcctcaaagcatatgctaaatcttttgtgcatagttgtagtatttaagttcagtcttgtatattgactttgtatgcttaaaactgcagGTTATATCAGGGAAGCTCTATGCCGGTCCTGAGGTGGACGTCTGGAGCTGTGGCGTTATTCTGTATGCTCTCTTGTGTGGCTCGTTGCCCTTCGACGACG
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atgcatgccttcaataatcacga-atgtaactaatcaggaatgcatgcctttaataataatcatgaatgtaacccccaaaccccaaaaaat-aaacccccagGTGATTAGCGGCAAGCTGTATGCGGGCCCGGAGGTGGACGTGTGGAGCTGCGGCGTCATTCTGTACGCGCTGTTGTGTGGATCACTGCCCTTTGACGACGMapped 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|162161228|gb|FC337291.1|FC337291EST: GTCACTTTCTCAAAACTAGTTGCGGAAGCCCCAATTATGCTGCTCCAGAG GTTATATCAGGGAAGCTCTATGCCGGTCCTGAGGTGGACGTCTGGAGCTGT
genomic: GTCACTTTCTCAAAACTAGTTGCGGAAGCCCCAATTATGCTGCTCCAGAGgttttcctcc ... aaaactgcagGTTATATCAGGGAAGCTCTATGCCGGTCCTGAGGTGGACGTCTGGAGCTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgtagtatttaagttcagtcttgtatattgactttgtatgcttaaaactgcagGTTATATCAGGGAAGCTCTATGCCGGTCCTGAGGTGGACGTCTGGAGCTGTGGCGTTATTCTGTATGCTCTCTTGTGTGGCTCGTTGCCCTTCGACGACG
tattgac putative branch site (score: 2)
tatttaagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acattgtacaaatcctcaaagcatatgctaaatcttttgtgcatagttgtagtatttaagttcagtcttgtatattgactttgtatgcttaaaactgcagGTTATATCAGGGAAGCTCTATGCCGGTCCTGAGGTGGACGTCTGGAGCTGTGGCGTTATTCTGTATGCTCTCTTGTGTGGCTCGTTGCCCTTCGACGACG
- - - - - - - - - - -catatgc