Sequence
atgc intronic sequence ATGC exonic sequence...gcccgtggggtgtgataatttcacagcagcatatcccgcagcacggctgggagtcatttagatagtcacagtttatgacaaggttgagccacacgtgcagGTTGTCGAGATCAACAGAGGGAGCAAGGTGAAGTACGAGCTTGACAAGAAGAGCGGTCTGATGAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S552_1V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os05g36260.1 (Oryza sativa), 3'ss of exon 1
-------------------------gcccgtggggtgtgataatttcacagcagcatatcccgcagcacggctgggagtcatttagatag-----tcacagtttatgacaaggttgagccacacgtgcagGTTGTCGAGATCAACAGAGGGAGCAAGGTGAAGTACGAGCTTGACAAGAAGAGCGGTCTGATGAAG
|| | | || | | | || || |||| | | || || || | | | | | | ||| || | ||||| || ||||||| || ||||||||||||||||||||||| |||||||||| || || || |||
gtaagtgcacgccctgttcttttgcatcctcctccagctccagcttaattattccgttctttgccgcccggccgctggcgatgatgacagctttgttgcgatgtgtcccgtggtggatttttg-gcacagGTCGTGGAGATCACCAAGGGGAGCAAGGTGAAGTACGAGCTGGACAAGAAGACGGGGCTCATCAAG
upper sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 3
gcccgtggggtgtg-ataattt-cacagcagcatatcccgcagcacg-gctgggagtcattt-agatagtcacagtttatgacaaggttgagccacacgtgcagGTTGTCGAGATCAACAGAGGGAGCAAGGTGAAGTACGAGCTTGACAAGAAGAGCGGTCTGATGAAG
| | |||| ||||| | || || || | |||| ||| || | |||| || | | | ||||| | || || ||||||| ||||||| | |||||||| |||||||| |||||||||||||||| || |||| |||
gtaagcatcgtgttcataatatatttgtcatcaaatt--gaagcaaacactgcgatttatttcaggatgcatctggacctgacatgtttttttt-----tgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG
upper sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 2
------gcccgtggggtgtgataatttcacagcagcatatcccgcagcacggctgggagtcatttagatagtcacagtttatgacaaggttgagccacacgtgcagGTTGTCGAGATCAACAGAGGGAGCAAGGTGAAGTACGAGCTTGACAAGAAGAGCGGTCTGATGAAG
|||| | || | | | || || | | | | | ||| || || | || | |||| | | ||||||| |||||| || || |||||||||||||||||||| |||||||| | || | || | |
gtaagcgccctcgccacatgcca----cgccacaagggattcttcccttggatttacactcacttgactaacgatgcgtttcttcttggtt---ttgcgtggatagGTTGTGGAGATCTCCAAGGGAAGCAAGGTGAAGTACGAGCTCGACAAGAAAACGGGGTTCATCATG
upper sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G026470_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------gcccgtggggtgtgataatttcac---agcagcatatcc-----cgcagcacggctgggagtcatttagatagtca-----cagtttatgacaaggttgagccacacgtgcagGTTGTCGAGATCAACAGAGGGAGCAAGGTGAAGTACGAGCTTGACAAGAAGAGCGGTCTGATGAAG----------------------------------
|| | | | | | || | | | ||| | | ||| | ||| || || | | | | || | || || | ||| |||||| || ||||||| || ||||||||||||||||||||||| |||||||||| || || || |||
gtaagtatctgacgaatcccattccccagacccctcaccccagcaagcaagcaagcaagcagccaaagttgttctcgatcgacatgtgtgaatatggagcgtgtctgacgatccttccggtgcgcgtccgtccgtccgttacgtacgtggtgccgacgagcagGTCGTGGAGATCACCAAGGGGAGCAAGGTGAAGTACGAGCTGGACAAGAAGACGGGGCTCATCAAGGTGGACCGGATCCTCTACTCGTCCGTCGTCTACC
upper sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 2
-gcccgtggggtgtgataatttcacagcagcatatcccgcagcacggctgggagtcatttagatagtcacagtttatgacaaggttgagccacacgtgcagGTTGTCGAGATCAACAGAGGGAGCAAGGTGAAGTACGAGCTTGACAAGAAGAGCGGTCTGATGAAG
| |||| | |||| | ||| | | | | | | | | || |||| | || | | | | ||| | | |||||||||| ||||||| | ||| |||||||| ||||| || ||||||||||||| || |||| |||
tatagcaattgcatgatgacaccacacctatataattccattcttgatttgcatttagttttctagtaaaagggtgtttct-gcttgttcaatggctgcagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAGTATGAACTTGACAAGAAGACTGGATTGATTAAG
upper sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ33440 (Selaginella moellendorffii), 3'ss of exon 2
gcccgtggggtgtgataatttcacagcagcatatcccgcagcacggctgggagtcatttagatagtcacagtttatgacaaggttgagccacacgtgcagGTTGTCGAGATCAACAGAGGGAGCAAGGTGAAGTACGAGCTTGACAAGAAGAGCGGTCTGATGAAG
|| ||| || | | | ||| ||| | || ||| || | ||| | ||||||||||| ||||||| || ||| |||| ||||| |||||||| ||||||||||| ||||| || |||
------------------------------gtaagtcgctgcccattttcc-gcgatt--gatc-ttgagcttgatggtgag-tgaggcctcgtgtgcagGTTGTGGAGATCAGCAAAGGAGGCAAAGTGAAATACGAGCTGGACAAGAAGAGTGGTCTCATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctgggagtcatttagatagtcacagtttatgacaaggttgagccacacgtgcagGTTGTCGAGATCAACAGAGGGAGCAAGGTGAAGTACGAGCTTGACAAGAAGAGCGGTCTGATGAAG
atttagata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcccgtggggtgtgataatttcacagcagcatatcccgcagcacggctgggagtcatttagatagtcacagtttatgacaaggttgagccacacgtgcagGTTGTCGAGATCAACAGAGGGAGCAAGGTGAAGTACGAGCTTGACAAGAAGAGCGGTCTGATGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG