Sequence
atgc intronic sequence ATGC exonic sequence...taagaagtttcaaatatggaacataatatcttttctttccaatgtttggggcaagaaaagacatcttttgtatccaatattatgattggcccttttgcagGAAGTAACCGGCGTCAAGTAAAATCGGTGGTCATTGGCAGACCAATTTTACTAGCTTTGGAAGATATTGACGGAAGTCCTTCTTTTCTGGAGAAAGCCCT
Basic information
species | Physcomitrella patens |
transcript | PP1S78_26V6.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S78_26V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA06G09860.1 (Glycine max), 3'ss of exon 8
taagaagtttcaaatatggaacataatatc-ttttctttccaatgtttggggcaagaaaagacatctttt-gtatccaatattatgatt----ggcccttttgcagGAAGTAACCGGCGTCAAGTAAAATCGGTGGTCATTGGCAGACCAATTTTACTAGCTTTGGAAGATATTGACGGAAGTCCTTCTTTTCTGGAGAAAGCCCT
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------acctccgtcgtgaatttttatgtgatgatacttgtacttaatgcagtaaaagatgataactttttatttcctttgatatgatttttctgcacttctatagTGAAGGATAGAGAACCAGTTAAGTCTACTGTCGTTGGCCGGCCAATTTTACTTGCTTTGGAGGATGTTGATGGAACTCCATCATTTTTGGAGAAAGCCCT
upper sequence: PP1S78_26V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA04G09780.1 (Glycine max), 3'ss of exon 5
taagaagtttcaaatatggaacataatatcttttctttccaatgtttggggcaagaaaagac----atcttttgtatccaatattatgatt----ggcccttttgcagGAAGTAACCGGCGTCAAGTAAAATCGGTGGTCATTGGCAGACCAATTTTACTAGCTTTGGAAGATATTGACGGAAGTCCTTCTTTTCTGGAGAAAGCCCT
||| || | | || | | | | | || || ||| |||||| | || | | ||| | ||||||| || ||| | || | | | | ||| ||||| || ||||| | ||||||||||| |||||||| ||| |||| |||| ||| || ||| |||||||||||||
------acctcagtcttgaatttt--tacgtgatgatactagtgcttaatgcagtaaaagatgataactttatatttcctttgatatgatttttctgcacttctatagTGAAGGATAGAGAACCAGTTAAATCTACCGTTGTTGGCCGGCCAATTTTACTTGCTTTGGAGGATGTTGATGGAACTCCATCATTTTTGGAGAAAGCCCT
upper sequence: PP1S78_26V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv00s0199g00070.t01 (Vitis vinifera), 3'ss of exon 10
--taagaagtttcaaatatggaacata-atatcttttctttccaatgtttggggcaagaaaagacatcttttgtatccaatattatgattggcccttttgcagGAAGTAACCGGCGTCAAGTAAAATCGGTGGTCATTGGCAGACCAATTTTACTAGCTTTGGAAGATATTGACGGAAGTCCTTCTTTTCTGGAGAAAGCCCT
| | |||| || ||| | ||| | | || | | | | ||| | | ||| || || | || || || || | | || ||||| || |||| |||| || ||||||||||| |||||||||||| || ||||| ||| ||||| |||||||||||||
tgtgtgtgtcacttgatattgatcatttgtggttttccaaactgatctgtttgcttgggtgtttcat-tgggatgattaattttctg--tatttctgttctagTGAGGAGTAAACATCCTGTAAAGTCCTTGGTGGTTGGTAGGCCAATTTTACTTGCTTTGGAAGATGTTAACGGAGCTCCATCTTTCTTGGAGAAAGCCCT
upper sequence: PP1S78_26V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ23838 (Selaginella moellendorffii), 3'ss of exon 6
taagaagtttcaaatatggaacataatatcttttctttccaatgtttggggcaagaaaagacatcttttgtatccaatattatgattggcccttttgcagGAAGTAACCGGCGTCAAGTAAAATCGGTGGTCATTGGCAGACCAATTTTACTAGCTTTGGAAGATATTGACGGAAGTCCTTCTTTTCTGGAGAAAGCCCT
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------------------------------gtgcctgtaggaattttagttttctagcgagctgctgacttgacattttcttttcttttttttctggtagGGAAAGATAGAAGATCCGTCAAGTCAATGGTTGTCGGTAGACCGATTTTACTTGCTTTGGAAGACATTGACGGTAGTCCATCGTTCCTGGAGAAGGCTTT
upper sequence: PP1S78_26V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ24423 (Selaginella moellendorffii), 3'ss of exon 6
taagaagtttcaaatatggaacataatatcttttctttccaatgtttggggcaagaaaagacatcttttgtatccaatattatgattggcccttttgcagGAAGTAACCGGCGTCAAGTAAAATCGGTGGTCATTGGCAGACCAATTTTACTAGCTTTGGAAGATATTGACGGAAGTCCTTCTTTTCTGGAGAAAGCCCT
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---------------gtgcctgtaggaattttagttttccagcgagctgc---tgacttgacattttctttttcttttttttt---------tctggtagGGAAAGACAGAAGATCCGTCAAGTCAATGGTTGTCGGTAGACCAATTTTACTTGCTTTGGAAGACATTGACGGTAGTCCATCGTTCCTGGAGAAGGCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggggcaagaaaagacatcttttgtatccaatattatgattggcccttttgcagGAAGTAACCGGCGTCAAGTAAAATCGGTGGTCATTGGCAGACCAATTTTACTAGCTTTGGAAGATATTGACGGAAGTCCTTCTTTTCTGGAGAAAGCCCT
cccttttgc CT-rich tract
aatattatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taagaagtttcaaatatggaacataatatcttttctttccaatgtttggggcaagaaaagacatcttttgtatccaatattatgattggcccttttgcagGAAGTAACCGGCGTCAAGTAAAATCGGTGGTCATTGGCAGACCAATTTTACTAGCTTTGGAAGATATTGACGGAAGTCCTTCTTTTCTGGAGAAAGCCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA