Sequence
atgc intronic sequence ATGC exonic sequencegttagtttcgtaaacgttgctgcccaagtggttcactatgctcataaattccctataacactttctaaatcagcacttccttcttctcatgaaggtcactcctttcgttgtgctatgaaaggcctcttgatttcctgttcgttttgcatgcagGCAAGAGTGCACTTGCACTCCTGTGCACTATTTTGTAATATTATCAATGCAAAGATCAGGAAGTGGATGGTTTGAGACTCTACTCAATAATCACCCAAAT
Basic information
species | Physcomitrella patens |
transcript | PP1S310_50V6.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S310_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os03g24910.1 (Oryza sativa), 3'ss of exon 3
gttagtttcgtaaacgttgctgcccaagtggttcactatgctcataaattccct-ataacactttctaaatcagcacttccttcttctcatgaaggtcactcctttcgttgtgctatgaaag-gcctcttgatttcctgttcgttttgcatgcagGCAAGAGTGCACTTGCACTCCTGTGCACTATTTTGTAATATTATCAATGCAAAGATCAGGAAGTGGATGGTTTGAGACTCTACTCAATAATCACCCAAAT
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-------------------------------------------gtaattttctagatagaatctcttgtgttaa----tcctgtgctacattata--catttcctttgttatttttttcatgtgcattctgacaatattttctcattg---acagGGGGGAATGCGCGTGTACTCCAGTTCGGTTTTTTGTTATCATTTCTATGCAAAGATCAGGAAGTGGGTGGTTTGAGACTTTGCTAAATAGCCATCCCAAT
upper sequence: PP1S310_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G055607_T01 (Zea mays), 3'ss of exon 3
gttagtttcgtaaacgttgctgcccaagtggttcactatgctcataaattccctataacactttctaaatcagcacttccttcttctcatgaaggtcactcctttcgttgtgctatgaaaggcctcttgatttcctgttcgttttgcatgcagGCAAGAGTGCACTTGCACTCCTGTGCACTATTTTGTAATATTATCAATGCAAAGATCAGGAAGTGGATGGTTTGAGACTCTACTCAATAATCACCCAAAT
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----------------------------------gtaagatccaccacttgactgtgaggagatataaaat----ctttgcattcctcaattatgtagtacagtatattttg---tggctgatgttgatattttttgtct-ttctgc-tgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCAAAGATCGGGAAGTGGATGGTTTGAGACCTTGATGAATAGTCACCCTAAC
upper sequence: PP1S310_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA14G08870.1 (Glycine max), 3'ss of exon 2
gttagtttcgtaaacgttgctgcccaagtggttcactatgctcataaattccctataacactttctaaatcagcacttccttcttctcatgaaggtcactcctttcgttgtgctatgaaaggcctcttgatttcctgttcgttttgcatgcagGCAAGAGTGCACTTGCACTCCTGTGCACTATTTTGTAATATTATCAATGCAAAGATCAGGAAGTGGATGGTTTGAGACTCTACTCAATAATCACCCAAAT
| | ||| | | | || || || | || | || | | ||| | | || | | || | |||| | | | | | |||| | ||||| |||||| |||||| | | |||| ||||| |||||||||||||||| ||||||||||||||||| | | || | ||| |||
------------------------------------------------atgcatatg-ctttgtggaatgcaaatttttcaatttgctacaaatatttgttatttgggtttgattatatagctatattgaat----gattggtgaatgagcagAGAGGAGTGTGCTTGCAATCCTGTCCGGTTTTTTACCATATTGACAATGCAAAGATCAGGTAGTGGATGGTTTGAGACGTTGTTGAACAGTCATATGAAT
upper sequence: PP1S310_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA17G36300.1 (Glycine max), 3'ss of exon 1
gttagtttcgtaaacgttgctgcccaagtggttcactatgctcataaattccctataacactttctaaatcagcacttcctt--cttctcatgaaggtcactcctttcgttgtgctatgaaaggcctcttgatttcctgttcgttttgcatgcagGCAAGAGTGCACTTGCACTCCTGTGCACTATTTTGTAATATTATCAATGCAAAGATCAGGAAGTGGATGGTTTGAGACTCTACTCAATAATCACCCAAAT
||| |||| | | || || || |||||| | | | | | | || || || | | ||| || | | | |||| | ||||| |||||| |||||| | | |||||| ||||| ||||||||||||| || ||||||||||||||||| | | || | ||| |||
---------------------------------------------------tgcata-tgctttgaggaagaaattttttttaattttccatgaacattaattcatgtgc-gtttgattaattagttat--attgaatgattggtgaatgagcagAGAGGAGTGTGCTTGCAATCCTGTACGGTTTTTTGTCATATTGACAATGCAAAGATCGGGGAGTGGATGGTTTGAGACGTTGTTGAACAGTCATATGAAT
upper sequence: PP1S310_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv07s0031g00880.t01 (Vitis vinifera), 3'ss of exon 3
gttagtttcgtaaacgttgctgcccaagtggttcactatgctcataaattccctataacactttctaaatcagcacttccttcttctcatgaaggtcactcctttcgttgtgctatgaaaggcctcttgatttcctgttcgttttgcatgcagGCAAGAGTGCACTTGCACTCCTGTGCACTATTTTGTAATATTATCAATGCAAAGATCAGGAAGTGGATGGTTTGAGACTCTACTCAATAATCACCCAAAT
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----------------------------------------------------------------gtaactta-caattgatgcattaggttttgaatttgggctcccttgtgaaaatgaatttgcccatttttcatttggggtgtgcttgcagGGCTGAATGTGCAAATAATCCTGTGAGATTCTTTGCCATAGTGTCGATACAGAGATCAGGAAGTGGATGGTTTGAGACACTATTAAATAGTCATATTAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcctttcgttgtgctatgaaaggcctcttgatttcctgttcgttttgcatgcagGCAAGAGTGCACTTGCACTCCTGTGCACTATTTTGTAATATTATCAATGCAAAGATCAGGAAGTGGATGGTTTGAGACTCTACTCAATAATCACCCAAAT
tcttgat putative branch site (score: 4)
tttcctgttcgtttt CT-rich tract
tatgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtttcgtaaacgttgctgcccaagtggttcactatgctcataaattccctataacactttctaaatcagcacttccttcttctcatgaaggtcactcctttcgttgtgctatgaaaggcctcttgatttcctgttcgttttgcatgcagGCAAGAGTGCACTTGCACTCCTGTGCACTATTTTGTAATATTATCAATGCAAAGATCAGGAAGTGGATGGTTTGAGACTCTACTCAATAATCACCCAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA