Sequence
atgc intronic sequence ATGC exonic sequence...caaaaaacttttcagagtttgccagtgaacgaatattttgtagaaagtacttcccctctgtataaggaaagggctgatgggagtgtaaattattgtgcagTCTCCGCACATCACTTTGTCTACAATTTAAGCCTCATCATATTGCTGCGGGGGCTATCTTCCTGGCTGCTAAGTTTCTGAAGGTGAACTTGCCTGAGGAA
Basic information
| species | Physcomitrella patens |
| transcript | PP1S119_132V6.2 |
| intron # | 7 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S119_132V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os12g30020.1 (Oryza sativa), 3'ss of exon 5
caaaaaacttttcagagtttgccagtga-acgaatatt-ttgtagaaagtacttcccctctgtataaggaaagggctgatgggagtgtaaattattgtgcagTCTCCGCACATCACTTTGTCTACAATTTAAGCCTCATCATATTGCTGCGGGGGCTATCTTCCTGGCTGCTAAGTTTCTGAAGGTGAACTTGCCTGAGGAA
|| ||| | ||| || |||| | | | || | | | || || | | | | | ||| |||||| ||| || || || || ||||| || || || ||||||||||||||||| || || |||||||| |||||||||| ||||| || ||||| | || ||
----------------gtatgctattgatacccttattatctttagagatatcactcaatcatgtatataacacgttaaaaagggcgta---tattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT
upper sequence: PP1S119_132V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G308570_T02 (Zea mays), 3'ss of exon 13
caaaaaacttttcagagtttgccagtgaacgaatattttgtagaaagtacttcccctctgtataaggaaagggctgatgggagtgtaaattattgtgcagTCTCCGCACATCACTTTGTCTACAATTTAAGCCTCATCATATTGCTGCGGGGGCTATCTTCCTGGCTGCTAAGTTTCTGAAGGTGAACTTGCCTGAGGAA
|| ||| | | | | || || | || | | | | | | ||| ||||||| |||||||| |||||||| || |||||||| || || |||||||| || || || |||||||||||||| |||||||| || || || | || ||
----------------gtatgctaaaattactcttcatcactgcaaatagtaatccac---aaacatgcctacttactataccttaaaaggggtgtgcagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGGCGCAATCTTCCTGGCTGCGAAGTTTCTTAAAGTCAAGCTTCCATCAGAT
upper sequence: PP1S119_132V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G115670_T01 (Zea mays), 3'ss of exon 4
caaaaaacttttcagagtttgccagtga-acgaatatt----ttgtagaaagtacttcccctctgtataaggaaagggctgatgggagtgtaaattattgtgcagTCTCCGCACATCACTTTGTCTACAATTTAAGCCTCATCATATTGCTGCGGGGGCTATCTTCCTGGCTGCTAAGTTTCTGAAGGTGAACTTGCCTGAGGAA
|| ||| |||| || || | || | | | | ||| | ||| || | || | | ||| | ||| ||| || || || || ||||| || ||||| |||||||||||||||| || || |||||||| |||||||||| ||||| || ||||| | || ||
----------------gtatgctagtgctacccttactgtcgtttgaaattgcagttcacagttgtgtatctactacact--taatattgtg---cactgtacagACTGCGTACTTCGCTTTGCCTGCAATTCGAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT
upper sequence: PP1S119_132V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA15G41040.1 (Glycine max), 3'ss of exon 4
caaaaaacttttcagagtttgccagtgaacgaatattttgtagaaagtacttcccctctgtataaggaaagggctgatgggagtgtaaattattgtgcagTCTCCGCACATCACTTTGTCTACAATTTAAGCCTCATCATATTGCTGCGGGGGCTATCTTCCTGGCTGCTAAGTTTCTGAAGGTGAACTTGCCTGAGGAA
|| || | | || |||||| | | | || | | | | ||| | ||| | | ||||| || || ||||||||||| | ||||||||||||||||| ||||| || || || || ||||| ||||| ||||||||||||||||| | || |||
----------------gtatgaagattacacaaatttttgttaaggccagtggcctttgatttttctttcctga-aatgaggatgtga-----tatgcagACTTCGGACATCACTTTGCTTGCAATTTAAGCCTCATCACATTGCAGCTGGAGCCATATTCCTTGCTGCCAAGTTTCTGAAGGTGAAGCTACCATCGGAT
upper sequence: PP1S119_132V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA08G17960.1 (Glycine max), 3'ss of exon 4
caaaaaacttttcagagtttgccagtgaacgaatattttgtagaaagtacttcccctctgtataaggaaagggctgatgggagtgtaaattattgtgcagTCTCCGCACATCACTTTGTCTACAATTTAAGCCTCATCATATTGCTGCGGGGGCTATCTTCCTGGCTGCTAAGTTTCTGAAGGTGAACTTGCCTGAGGAA
|| || | | ||| |||| || | | ||| || | | || | | | | | ||||| || || ||||||||||| | ||||||||||| ||||| ||||| || || || || ||||| ||||| ||||||||||||||||| | || ||
----------------gtatgaagattacacaattttttttaaggcgagtgtggcctttgatttttct-----ttcctgaaattaggatgtgatatgcagACTTCGGACATCACTTTGCTTGCAATTTAAGCCCCATCACATTGCAGCTGGAGCCATATTCCTTGCTGCCAAGTTTCTGAAGGTGAAGCTACCATCAGAT
upper sequence: PP1S119_132V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT5G45190.1 (Arabidopsis thaliana), 3'ss of exon 5
caaaaaacttttcagagtttgccagtgaacgaatattttgtagaaagtacttcccctctgtataaggaaagggctgatgggagtgtaaattattgtgcagTCTCCGCACATCACTTTGTCTACAATTTAAGCCTCATCATATTGCTGCGGGGGCTATCTTCCTGGCTGCTAAGTTTCTGAAGGTGAACTTGCCTGAGGAA
|| || ||| | | | | || | || | | | ||||| | || | || ||| | |||||||| || ||||| || || || ||||||||||||||||||||||| || || || || || || || || ||||| || || ||||| || || ||
----gtacgttcaagaactatttcct---tctaaagcttccaataattctatgtgccttgtattttc----gtcttcatacaatgaaaagtggcttgcagTCTACGGACATCTCTCTGCCTGCAATTTAAGCCTCATCATATTGCGGCTGGTGCAATATTTCTTGCGGCCAAGTTCCTTAAAGTGAAGTTACCATCAGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtacttcccctctgtataaggaaagggctgatgggagtgtaaattattgtgcagTCTCCGCACATCACTTTGTCTACAATTTAAGCCTCATCATATTGCTGCGGGGGCTATCTTCCTGGCTGCTAAGTTTCTGAAGGTGAACTTGCCTGAGGAA
ggctgat putative branch site (score: 4)
tgtaaattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaaaaacttttcagagtttgccagtgaacgaatattttgtagaaagtacttcccctctgtataaggaaagggctgatgggagtgtaaattattgtgcagTCTCCGCACATCACTTTGTCTACAATTTAAGCCTCATCATATTGCTGCGGGGGCTATCTTCCTGGCTGCTAAGTTTCTGAAGGTGAACTTGCCTGAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
