Sequence
atgc intronic sequence ATGC exonic sequence...atttagcgctgattaaagaagccgacctttcaacgtcatcatatgcctttcattcgtaactccaagtatcttgccaaatgctaatactaggtaatatcagGTGCAGGCCTACTTATTTGATGGCTACTGGGAAGATATTGGAACTATTGAAGCTTTTTACAACGCAAACTTAGGAATCACGAAGAAGCCCGTTCCTGATT
Basic information
| species | Physcomitrella patens |
| transcript | PP1S2_337V6.1 |
| intron # | 4 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S2_337V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------------------atttagcgctgattaaagaagccgacctttcaacgtc-atcatatgcctttcattcgtaactccaag--tatcttgc-caaatgctaatactaggtaatat------cagGTGCAGGCCTACTTATTTGATGGCTACTGGGAAGATATTGGAACTATTGAAGCTTTTTACAACGCAAACTTAGGAATCACGAAGAAGCCCGTTCCTGATT
| | | | || || | | || || | | || | || ||| | ||| | || |||| |||| || || | |||| | ||||||| || ||||||| |||||| ||||||||||||||||| ||||| || || || ||||| || ||||| || || || ||||| || || || ||||
gtacgctatgctcttgaaacttgtagcatgtagggaatttttatccttctctcagttcatgctgtaggttttgtgaagtttggtatgtaaactgcagttacatcatttattgtgaaatgttacttctttacttaatttttactttgcatgtttgcttatgct-gctaatgtatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT
upper sequence: PP1S2_337V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G106213_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------------------------------atttag---cgctgattaaagaagccgacctttcaacgtcatc----atatgccttt-cattcgtaactccaagtatcttgccaaatgctaatactaggtaatatcagGTGCAGGCCTACTTATTTGATGGCTACTGGGAAGATATTGGAACTATTGAAGCTTTTTACAACGCAAACTTAGGAATCACGAAGAAGCCCGTTCCTGATT
|||| | | || || | | || | || || || ||| | || || ||| || | ||| | | | || | ||||||| || ||||||| |||||| ||||||||||||||||| ||||||||||| ||||| || |||||||| ||||| || |||||||| || || ||||
gtatgctctgctcttgagctttcttggtttctcttctccagtttttgtttttatcattctggatttatgatttgggcatttcggttgaaagattttaatttcatcatttattgaagatttggcttagcctttttagtagttgctatgtttgcttatgatgttgttgtgtt-caaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAAGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCTGTACCGGATT
upper sequence: PP1S2_337V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G163437_T01 (Zea mays), 3'ss of exon 4
-atttagcgctgattaaagaagccgacct--ttcaacgtcatcatatgcctttcatt-cgtaactccaagtatcttgccaaatgctaatactaggtaatatcagGTGCAGGCCTACTTATTTGATGGCTACTGGGAAGATATTGGAACTATTGAAGCTTTTTACAACGCAAACTTAGGAATCACGAAGAAGCCCGTTCCTGATT
|| | || | | | | |||| | | | || | | || | | | | || | | | ||||| ||||| || ||| |||||| || |||||||||||||| || ||||| || ||||| || |||||||| ||||| || |||||||| | || ||||
catgctagaaagcctaggcaggttgggttggctcaaggccggagggagggaagggttacaccttttaaaatggtatttaagaccttatttttgtctg----cagGTTCAGGCTTATCTATATGATGGTTATTGGGAAGATATTGGTACAATTGAGGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCAATACCAGATT
upper sequence: PP1S2_337V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 4
---------------atttagcgctgattaaagaagccgacctttcaacgtcat-catat--gcctttcattcgtaactcca-agtatcttgccaaatgctaatactaggtaatatcagGTGCAGGCCTACTTATTTGATGGCTACTGGGAAGATATTGGAACTATTGAAGCTTTTTACAACGCAAACTTAGGAATCACGAAGAAGCCCGTTCCTGATT
||| |||| || | | | ||| || | |||| ||| | || | || || ||| | | | || | |||||||| || ||||| | |||||||||||||||||| ||||| || ||||| ||||| || || ||||| | |||||||| || ||||| || ||||| |
gtatgtgttccttctggttatttaatattacgaaaactttcttgtcattttcttgcatagcaaaatttagcatgcaattttttagaatgttgtatggca-tgtttgtgtatattcacagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAGGCTTTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACT
upper sequence: PP1S2_337V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 4
---------------------atttagcgctgattaaagaagccgacctttcaacgtcatcatatgcctttcattcgtaactccaagtatcttgccaaatgctaatactaggtaatat----------------------------------------------------------------------------cagGTGCAGGCCTACTTATTTGATGGCTACTGGGAAGATATTGGAACTATTGAAGCTTTTTACAACGCAAACTTAGGAATCACGAAGAAGCCCGTTCCTGATT
|| | |||||||| || ||||| | |||||||||||||||||| ||||| || || || ||||| || || ||||| | |||||||| || ||||| || ||||| |
gtgattcctggtgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaactttcttgttattttcctgcatggtaaattagcatgcaattttttgagaatatgtacggcatgtttgtgtgtattcacagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATCGAGGCTTTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACT
upper sequence: PP1S2_337V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------------atttag-cgctgattaaagaagccgacctttcaacgtcatcatatgcctttcattcgtaactccaagtatcttgccaaa--tgctaatactaggta-----atatcagGTGCAGGCCTACTTATTTGATGGCTACTGGGAAGATATTGGAACTATTGAAGCTTTTTACAACGCAAACTTAGGAATCACGAAGAAGCCCGTTCCTGATT
| || | ||| | | | ||||| ||| || | | | | | | | | | | | || ||| |||||| | | | |||||||| || ||| ||| |||||| ||||||||||| ||||| ||||| || || ||||| ||||| || | |||||||| ||||| || ||||||||||
gtgagtgtttatattcatgtttacaacatctagtttgtattctgatgctcaagcaagtctctgttactctatggtttgctttcggattcaacagcttcttgtagctgattatgctatgcagaaggcaaaacctgctaactttgatcatgggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATT
upper sequence: PP1S2_337V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 4
atttagcgctgattaaagaagccgacc-tttcaacgtcatcatatgcctttcattcgtaactccaagt-atcttgccaaatgctaa--tactaggtaatatc---agGTGCAGGCCTACTTATTTGATGGCTACTGGGAAGATATTGGAACTATTGAAGCTTTTTACAACGCAAACTTAGGAATCACGAAGAAGCCCGTTCCTGATT
| | | | | | |||| | || || || ||| | |||| | ||| | ||| | | | || | || |||| || ||||||| || ||||| | |||||||||||||||||| ||||| || ||||| |||||||| ||||| || || || ||||| |||||||| || || ||||
----tatgatcactggaaattccgataatcaaaatgttattttat---ctgcatttgccttcttaagagaactttcatagagtcaaattgctgcataatctctgtagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAGGCTTTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATT
upper sequence: PP1S2_337V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ16157 (Selaginella moellendorffii), 3'ss of exon 4
atttagcgctgattaaagaagccgacctttcaacgtcatcatatgcctttcattcgta---actccaagtatcttgccaaatgctaatactaggta-atatcagGTGCAGGCCTACTTATTTGATGGCTACTGGGAAGATATTGGAACTATTGAAGCTTTTTACAACGCAAACTTAGGAATCACGAAGAAGCCCGTTCCTGATT
| || ||| | | | | || | | || | | | |||||| || | |||||||| || || || | |||||| ||||||||||| || || ||||| || || |||||| | || ||||||||| |||| |||||||||||||| | |
----------------------------------------gtttgtttttgctctgaagggatcgaaacgaacgtgacttaaac-aatactctgttcgttgcagGTGCAAGCGTATTTGTATGATGGATACTGGGAAGACATAGGGACTATAGAGGCATTTTACCATGCCAACTTAGGATTCACAAAGAAGCCCGTTCCAAACT
upper sequence: PP1S2_337V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ18043 (Selaginella moellendorffii), 3'ss of exon 4
atttagcgctgattaaagaagccgacctttcaacgtcatcatatgcctttcattcgtaactccaagtatcttgccaaatgctaatactaggtaatatcagGTGCAGGCCTACTTATTTGATGGCTACTGGGAAGATATTGGAACTATTGAAGCTTTTTACAACGCAAACTTAGGAATCACGAAGAAGCCCGTTCCTGATT---
| ||| | || | | || || || || | || || || | | ||| | || ||| || |||||| | |||||||| |||||||| |||||||| || || || ||||||||||| || ||| ||||| | || |||| || |||||| |
--------------------gtaagttttttttcttcttt-tgtgtctctct----caagcctttgtgattttttaatcttttgttctactttcta---gGTACAAGCCTACCTGTTTGATGGATACTGGGAGGATATTGGCACAATCGAGGCTTTTTACAATGCCAACATAGGATTGACTAAGAGCCC---TCCTGAATTTA
upper sequence: PP1S2_337V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ09564 (Selaginella moellendorffii), 3'ss of exon 3
atttagcgctgattaaagaagccgacctttcaacgtcatcatatgcctttcattcgtaactccaagtatcttgccaaatgctaatactaggtaatatc----agGTGCAGGCCTACTTATTTGATGGCTACTGGGAAGATATTGGAACTATTGAAGCTTTTTACAACGCAAACTTAGGAATCACGAAGAAGCCCGTTCCTGATT---
|| | | | | | | || ||| | ||| | | |||| | || || |||| || |||||| | |||||||| |||||||| |||||||| || || || ||||||||||| || ||| ||||| | || |||| || |||||| |
----------------------------------gtaagtttttttttcttttgtgtctctctcaagcctttgtgattttttaatcttttgttctactttctagGTACAAGCCTACCTGTTTGATGGATACTGGGAGGATATTGGCACAATCGAGGCTTTTTACAATGCCAACATAGGATTGACTAAGAGCCC---TCCTGAATTTA
upper sequence: PP1S2_337V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ17026 (Selaginella moellendorffii), 3'ss of exon 4
atttagcgctgattaaagaagccgacctttcaacgtcatcatatgcctttcattcgta---actccaagtatcttgccaaatgctaatactaggtaatatcagGTGCAGGCCTACTTATTTGATGGCTACTGGGAAGATATTGGAACTATTGAAGCTTTTTACAACGCAAACTTAGGAATCACGAAGAAGCCCGTTCCTGATT
| || ||| | | | | || | | || | | | | | | | |||||||| || || || | |||||| ||||||||||| || || ||||| || || |||||| | || ||||||||| |||| |||||||||||||| | |
----------------------------------------gtttgtttttgctctgaagggatcgaaacgaacgtgacttaaacaatgctctgttcgtcgcagGTGCAAGCGTATTTGTATGATGGATACTGGGAAGACATAGGGACTATAGAGGCATTTTACCATGCCAACTTAGGATTCACAAAGAAGCCCGTTCCAAACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctttcattcgtaactccaagtatcttgccaaatgctaatactaggtaatatcagGTGCAGGCCTACTTATTTGATGGCTACTGGGAAGATATTGGAACTATTGAAGCTTTTTACAACGCAAACTTAGGAATCACGAAGAAGCCCGTTCCTGATT
tgctaat putative branch site (score: 2)
taatacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttagcgctgattaaagaagccgacctttcaacgtcatcatatgcctttcattcgtaactccaagtatcttgccaaatgctaatactaggtaatatcagGTGCAGGCCTACTTATTTGATGGCTACTGGGAAGATATTGGAACTATTGAAGCTTTTTACAACGCAAACTTAGGAATCACGAAGAAGCCCGTTCCTGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaatgc
