Sequence
atgc intronic sequence ATGC exonic sequence...gttttcccgctcgacattcctccgctggtgtttttccactttcggtgtgaatactgggagtctattgactggctcgcatgcgctttattgtggaatctagGCAGCTGTGAGTGCACTTAAGCAATTTCCTGCAGTAAATGCGGTAATCGATGGAGATGATATCATATACAGAGACTACATTGACATCAGCATTGCTGTTG
Basic information
| species | Physcomitrella patens |
| transcript | PP1S2_220V6.1 |
| intron # | 6 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S2_220V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 10
gttttcccgctcgacattcctccgctggtgtttttccactttcggtgtg-aatactgggagtctattgactggctcgcatgcgctttattgtggaatctagGCAGCTGTGAGTGCACTTAAGCAATTTCCTGCAGTAAATGCGGTAATCGATGGAGATGATATCATATACAGAGACTACATTGACATCAGCATTGCTGTTG
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---gtactgaccaatcttg-tgtactgctgaagctgaactattgcttggtaattttactaatatattcaatg-tgctcgttccatttgctttg----tcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG
upper sequence: PP1S2_220V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G079538_T02 (Zea mays), 3'ss of exon 11
gttttcccgctcgacattcctccgctggtgtttttccactttcggtgtgaatactgggagtctat-tgactggctcgcatgcgctttattgtggaatctagGCAGCTGTGAGTGCACTTAAGCAATTTCCTGCAGTAAATGCGGTAATCGATGGAGATGATATCATATACAGAGACTACATTGACATCAGCATTGCTGTTG
| || || || | | | || | ||| || |||||| || ||| || ||| ||||| ||||| ||||||| | | || || ||||| || || ||||| ||||| |||||||||||||||||| | |||||||| |||||||||
-----------------gtatttgccagtcttaggcgttgcaaagcttttgcaccatacttttatgtggctggcta--attatatttgttttgg----tagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTG
upper sequence: PP1S2_220V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT5G55070.1 (Arabidopsis thaliana), 3'ss of exon 12
gttttcccgctcgacattcctccgctggtgtttttccactttcggtgtgaatactgggagtctattgactggctcgcatgcgctttattgtggaatctagGCAGCTGTGAGTGCACTTAAGCAATTTCCTGCAGTAAATGCGGTAATCGATGGAGATGATATCATATACAGAGACTACATTGACATCAGCATTGCTGTTG
| | || ||||| | | ||| ||| || | || | | | | | | | | | |||| ||||| ||||| || |||| |||| ||||||||| || |||||||||||||||||||| |||||||||||| | || ||||| || |||||||
-----------gtatggtaaaaaactcaaaagtttcctgaactatttagcatatcaggactcaaccgattaagtaatcttc-ttgaactatttgtttcagGCTGCTGTTAGTGCCCTCCAGCACCAACCTGTAGTAAATGCAGTTATCGATGGAGATGATATCATTTACAGAGACTACGTGGATATCAGTATCGCTGTTG
upper sequence: PP1S2_220V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ31629 (Selaginella moellendorffii), 3'ss of exon 6
gttttcccgctcgacattcctccgctggtgtttttccactttcggtgtgaatactgggagtctattgactggctcgcatgcgctttattgtggaatctagGCAGCTGTGAGTGCACTTAAGCAATTTCCTGCAGTAAATGCGGTAATCGATGGAGATGATATCATATACAGAGACTACATTGACATCAGCATTGCTGTTG
||||| ||| || | | || | | | | || | | | ||||| ||||| || || | || || | ||||| || || ||||| |||||||| ||||| |||||||||||| | |||||||||||||||||||
-------------------------------------gtattcggcgtggattgcgtaattcaagagtttctttttgctgacagacgtcat----tttagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTG
upper sequence: PP1S2_220V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ38519 (Selaginella moellendorffii), 3'ss of exon 6
gttttcccgctcgacattcctccgctggtgtttttccactttcggtgtgaatactgggagtctattgactggctcgcatgcgctttattgtggaatctagGCAGCTGTGAGTGCACTTAAGCAATTTCCTGCAGTAAATGCGGTAATCGATGGAGATGATATCATATACAGAGACTACATTGACATCAGCATTGCTGTTG
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-------------------------------------gtattcggcgtggattgcttaattcaagagtttctttttgctgacagacgtcat----tttagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgaatactgggagtctattgactggctcgcatgcgctttattgtggaatctagGCAGCTGTGAGTGCACTTAAGCAATTTCCTGCAGTAAATGCGGTAATCGATGGAGATGATATCATATACAGAGACTACATTGACATCAGCATTGCTGTTG
tattgac putative branch site (score: 2)
tttattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttcccgctcgacattcctccgctggtgtttttccactttcggtgtgaatactgggagtctattgactggctcgcatgcgctttattgtggaatctagGCAGCTGTGAGTGCACTTAAGCAATTTCCTGCAGTAAATGCGGTAATCGATGGAGATGATATCATATACAGAGACTACATTGACATCAGCATTGCTGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgcatgc
