Sequence
atgc intronic sequence ATGC exonic sequencegtgattctcccctctggtggcattctcaattgcagtttgtgtttaggattccttactctcttggtttttcaatatcaaaggtcattgcattgaaattgtgaaagaaggtttgatgtttttcgtgccaagaatttgagcactaatataatgtttgtgtagGTGGATATATATGAGTTGCGGAAGTTTATCGGTGGAAAAGCAGGGTCCTTCAAAGACAAGAATGGAAACCATATCGAGATGGGGCTGCACGTCTTTTTTG
Basic information
species | Physcomitrella patens |
transcript | PP1S149_171V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S149_171V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g10490.1 (Oryza sativa), 3'ss of exon 2
gtgattctcccctctggtggcattctcaattgcagtttgtgtttaggattccttactctcttggtttttcaatatcaaaggtcattgcattgaaattgtgaaagaaggtttgatgtttttcgtgccaagaatttgagcactaatataatgtttgtgtagGTGGATATATATGAGTTGCGGAAGTTTATCGGTGGAAAAGCAGGGTCCTTCAAAGACAAGAATGGAAACCATATCGAGATGGGGCTGCACGTCTTTTTTG
| ||| | | | ||| | |||| | ||| || || || || | | ||||| || || ||| | | || | || || |||| ||| | || |||| ||| ||||||||| || |||| || || || || | ||| || |||||||||||||||||||||||||| || || |
----------------------------------------------gtttcttcaattcattg--cctgcaatg----atgtccgtgttctgctcttccagggaaaagacagtgatttttggtttaccaaaattgggg--tgatgttcctcttttgcagGTTGATCTGTACGAGTCCCGGCCGTTTATCGGCGGCAAAGTCGGTTCTTTTGTGGATAGGAAAGGGAACCATATCGAGATGGGGCTGCACGTGTTCTTCG
upper sequence: PP1S149_171V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G454952_T01 (Zea mays), 3'ss of exon 2
gtgattctcccctctggtggcattctcaattgcagtttgtgtttaggattccttactctcttggtttttcaatatcaaaggtcattgcattgaaattgtgaaagaaggtttgatgtttttcgtgccaagaatttgagcactaatataatgtttgtgtagGTGGATATATATGAGTTGCGGAAGTTTATCGGTGGAAAAGCAGGGTCCTTCAAAGACAAGAATGGAAACCATATCGAGATGGGGCTGCACGTCTTTTTTG
|| || || ||| || || | || | ||||| | | | ||| ||| | ||| | || || ||| | | | | ||| | || | |||| ||| | || |||| || |||||||||||| || | || ||||| |||| | | |||||||||||||||||||||||||| || || || |
---------------------gttagcagttttg--ttgctttcagcagagctaaac------gttttcttgtccaacaattcactgcttcctaataat---------cttactgatttcccta--atcatcccgagtgactgtggtctggcttaacagGTTGATTTGTACGAGTCCCGTCCGTTTATCGGTGGTAAGGTTGGCTCCTTTGTTGACAGGCAAGGAAACCATATCGAGATGGGGCTGCATGTGTTCTTCG
upper sequence: PP1S149_171V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ20342 (Selaginella moellendorffii), 3'ss of exon 2
gtgattctcccctctggtggcattctcaattgcagtttgtgtttaggattccttactctcttggtttttcaatatcaaaggtcattgcattgaaattgtgaaagaaggtttgatgtttttcgtgccaagaatttgagcactaatataatgtttgtgtagGTGGATATATATGAGTTGCGGAAGTTTATCGGTGGAAAAGCAGGGTCCTTCAAAGACAAGAATGGAAACCATATCGAGATGGGGCTGCACGTCTTTTTTG
| || | | | | | | | || | | | | | | ||||| |||| || || ||||| || ||| ||||||||||| | || || | | |||||||||| || ||||| ||||||||||| |||||||||||||||
---------------------------------------------------------------------------------------------------gtaaaaccggtcagcatgtctggaa--aatcctctcaagttttgt-ttttgttttgtcagGTTGACATTTATGATACCAGGTCGTTCATCGGTGGAAAGGTTGGATCATACCAAGACAAGAACGGGAACCACATCGAGATGGGATTGCACGTCTTTTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaggtttgatgtttttcgtgccaagaatttgagcactaatataatgtttgtgtagGTGGATATATATGAGTTGCGGAAGTTTATCGGTGGAAAAGCAGGGTCCTTCAAAGACAAGAATGGAAACCATATCGAGATGGGGCTGCACGTCTTTTTTG
cactaat putative branch site (score: 2)
actaatataatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattctcccctctggtggcattctcaattgcagtttgtgtttaggattccttactctcttggtttttcaatatcaaaggtcattgcattgaaattgtgaaagaaggtttgatgtttttcgtgccaagaatttgagcactaatataatgtttgtgtagGTGGATATATATGAGTTGCGGAAGTTTATCGGTGGAAAAGCAGGGTCCTTCAAAGACAAGAATGGAAACCATATCGAGATGGGGCTGCACGTCTTTTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG