Sequence
atgc intronic sequence ATGC exonic sequence...tttttaaactggctcttcgagtcctggatcggtacttgcaacttcttggacacttcttgcacttgacgttgataaaacatttgactgaaaaatttggcagGCAACCATCGGTATCGATTTTCTCTCCAAGACAATGTATCTTGAAGACCGCACCGTTAGATTACAACTCTG
Basic information
species | Physcomitrella patens |
transcript | PP1S2_143V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S2_143V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os03g09140.1 (Oryza sativa), 3'ss of exon 1
----------------------------tttttaaactggctcttcgagtcctggatcggtacttgcaacttcttggaca-------cttcttgcacttgacgttgataaaacatttg-----actgaaaaatttggcagGCAACCATCGGTATCGATTTTCTCTCCAAGACAATGTATCTTGAAGACCGCACCGTTAGATTACAACTCTG
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gttcgttgatgtcgcgcgcgtccccgatcgatcgatcttacgcgctggagagagttccagttttttttcttttttgggcaaggtttgttcgatgaatttgacggtgttcatgttgttgcggcggcggcggcggcgtgcagGCGACGATCGGGATCGATTTCCTCTCCAAGACGATGTACCTCGAAGACCGAACCGTACGGCTGCAGCTTTG
upper sequence: PP1S2_143V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA05G05860.1 (Glycine max), 3'ss of exon 1
------tttttaaactggctcttcgagtcctggatcggtacttgcaacttcttggacacttcttgcacttgacgttgataaaacatttgactgaaaaatttggcagGCAACCATCGGTATCGATTTTCTCTCCAAGACAATGTATCTTGAAGACCGCACCGTTAGATTACAACTCTG
|| || || | | | | | | | || | | | || | || | ||| | | | ||| | | ||||| || ||||||||||||||||| || || || |||||||||||||| || || ||| || | || | ||
tgcatattcttgaatta---catgcatttccattttcctaaattgagttgtttacaattttaccgtactcaaaactttgttttcttttccttttg---ctaaacagGCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG
upper sequence: PP1S2_143V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA17G16200.1 (Glycine max), 3'ss of exon 1
tttttaaactggctcttcgagtcctggatcggtacttgcaacttcttggacacttcttg----cacttgacgttgataaaacatttgactgaaaaatttggcagGCAACCATCGGTATCGATTTTCTCTCCAAGACAATGTATCTTGAAGACCGCACCGTTAGATTACAACTCTG
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-gacaacacattatgtgcaaata-taattctacacatgcatttagttgtttacattttgaccgtactcaaaactttccttttttttcccttttg--ctaaacagGCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAATTGTGMapped 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|100403885|gb|BY955150.1|BY955150EST: AGTATTATCACGCGATTCATGTATGATAAATTTNGACA-CACTTNAC-AN GCAACCATCGGTATCGATTTTCTCTCCAAGACAATGTATCTTGAAGAACG
genomic: AGTATTATCACGCGATTCATGTATGATAAATTT-GACAACACTT-ACCAGgttggcttct ... aatttggcagGCAACCATCGGTATCGATTTTCTCTCCAAGACAATGTATCTTGAAGACCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggacacttcttgcacttgacgttgataaaacatttgactgaaaaatttggcagGCAACCATCGGTATCGATTTTCTCTCCAAGACAATGTATCTTGAAGACCGCACCGTTAGATTACAACTCTG
atttgac putative branch site (score: 4)
ttgataaaacattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttaaactggctcttcgagtcctggatcggtacttgcaacttcttggacacttcttgcacttgacgttgataaaacatttgactgaaaaatttggcagGCAACCATCGGTATCGATTTTCTCTCCAAGACAATGTATCTTGAAGACCGCACCGTTAGATTACAACTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA