Sequence
atgc intronic sequence ATGC exonic sequencegtacttgcatgtggttttccagttactgtggctattctaaaaatttttgtttcaagttttgtaatcgaattcttaagttttattcaacctcattcatgactaagaaaaaatcagaaaaagcaatgctgcctgtctgacagcgatcgattgtatgctttaacgctaacaagtcatatgatactatgaatgtaggtggccagTGCAGAGGCTTTGGTGGTTAGAGTTGTATCCTCCGTGGACAAGAAGCTGGAAGTCAAACAACGGTTCTTGGAAATTTTTCAAGGAGATTATCCAACTGAG
Basic information
species | Physcomitrella patens |
transcript | PP1S404_36V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S404_36V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 8
gtacttgcatgtggttttccagttactgtggctattctaaaaatttttgtttcaagttttgtaatcgaattcttaagttttattcaacctcattcatgactaagaaaaaatcagaaaaagcaatgctgcctgtctgacagcgatcgattgtat-gctttaacgctaacaagtcatatgatactatgaatgtaggtggccagTGCAGAGGCTTTGGTGGTTAGAGTTGTATCCTCCGTGGACAAGAAGCTGGAAGTCAAACAACGGTTCTTGGAAATTTTTCAAGGAGATTATCCAACTGAG
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------------------------------------------------------------------------------------tgacttctctcctg--taattgagaat-agaccactgacttttgccgtcatgaaggaaattattctcatcacttttaaatt--ctatttattccttatt-tgt---tagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAGAAGCTGGAAGTAAAACCACGTTTTTTGGAAATTTTTCAAGAAGATAACT--------
upper sequence: PP1S404_36V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 7
gtacttgcatgtggttttccagttactgtggctattctaaaaatttttgtttcaagttttgtaatcgaattcttaagttttattcaac-ctcattcatgactaagaaaaaatcagaaaaagcaatgctgcctgtctgacagcgatcgattgtatgctttaacgctaacaagtcatatgatactatgaatgtaggtggccagTGCAGAGGCTTTGGTGGTTAGAGTTGTATCCTCCGTGGACAAGAAGCTGGAAGTCAAACAACGGTTCTTGGAAATTTTTCAAGGAGATTATCCAACTGAG
| |||| | | || |||| | ||| | | ||| || | | | ||| | || ||| | | | || |||| || |||| | | | || || | | ||||| |||||||| || || ||||| || |||||||| || |||| ||| || |||||||||||||||| ||| |
----------------------------------------------------------------------------gcattatgctgcacttattctttttgccatcaaatttgattcctggtatgatgtcctttcact--ccatcaa--gtccactt---------ctaattatgccttact-tg---gtagATTCCTGGAGCGGAAGGACTTGTGGTCAGAGTTGTTTCATCAGTGGATAAAAAGCTGGAGGTTAAACCACGTTTTTTGGAAATTTTTCAAGAAGACAACT--------
upper sequence: PP1S404_36V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 9
gtacttgcatgtggttttccagttactgtggctattctaaaaatttttgtttcaagttttgtaatcgaattcttaagttttattcaacctcattcatgactaagaaaaaatcagaaaaagcaatgctgcctgtctgacagcgatcgattgtatgctttaacgctaacaagtcatatgatactatgaatgtaggtggccagTGCAGAGGCTTTGGTGGTTAGAGTTGTATCCTCCGTGGACAAGAAGCTGGAAGTCAAACAACGGTTCTTGGAAATTTTTCAAGGAGATTATCCAACTGAG
|| | | | | | | || | | ||| ||||| ||| | || || ||| | | | | | ||| | | | | || || || || ||| || | | | |||| | | || | || | ||| || || | ||| ||| ||| | | ||| |||||||||| || || || |||||||||||||||||||||| || || | |||||||||| | ||| |
-------------gtaatttaatggtggagtttgtta-acgtttatttctttca---tttattttcacatctgcaagctct--ttatttttatttttctatttg------tttgatctagtgattct--ttgttaga-aacagtatattgaag---ctgactttgttttttctt-tgacttgatacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTT-------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattgtatgctttaacgctaacaagtcatatgatactatgaatgtaggtggccagTGCAGAGGCTTTGGTGGTTAGAGTTGTATCCTCCGTGGACAAGAAGCTGGAAGTCAAACAACGGTTCTTGGAAATTTTTCAAGGAGATTATCCAACTGAG
cgctaac putative branch site (score: 2)
atatgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttgcatgtggttttccagttactgtggctattctaaaaatttttgtttcaagttttgtaatcgaattcttaagttttattcaacctcattcatgactaagaaaaaatcagaaaaagcaatgctgcctgtctgacagcgatcgattgtatgctttaacgctaacaagtcatatgatactatgaatgtaggtggccagTGCAGAGGCTTTGGTGGTTAGAGTTGTATCCTCCGTGGACAAGAAGCTGGAAGTCAAACAACGGTTCTTGGAAATTTTTCAAGGAGATTATCCAACTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT