Sequence
atgc intronic sequence ATGC exonic sequencegtgatttcttggttttacttgtttatctatggactctcgtcagttctggtttaggatgttgttttgccttaacgcctttgtcatttacttaatttttccatgggtggagtcatcttgttcatttatcctggtcaaggctcttcattgactacaagatatcctgatacgtaatcacagATGTTTATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTCCAGCTAGCAAAGGAAAAAGCTCCCTGTATCATCTTCATTGATGAAGTAGATGCAATTG
Basic information
species | Physcomitrella patens |
transcript | PP1S340_7V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 5
gtgatttcttggttttacttgtttatctatggactctcgtcagttctggtttaggatgttgttttgccttaacgcctttgtcatttacttaatttttccatgggtggagtcatcttgttcatttatcctggtcaaggctcttcattg--actacaag-atatcctgatacgtaatcacagATGTTTATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTCCAGCTAGCAAAGGAAAAAGCTCCCTGTATCATCTTCATTGATGAAGTAGATGCAATTG
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--------------------------------------------------------------------------------acatatgaacagccttgccttcagaagtctatttatttactatttacttgcatatggttttctagcgcaacaataatcatatttttttgggcttgcccagATGTTTATCGGTGATGGAGCAAAGCTGGTTCGGGATGCTTTTCAGCTTGCTAAGGAGAAAGCTCCCTGCATCATTTTCATTGATGAGATTGATGCCATTG
upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 5
gtgatttcttggttttacttgtttatctatggactctcgtcagttctggtttaggatgttgttttgccttaacgcctttgtcatttacttaatttttccatgggtggagtcatcttgttcatttatcctggtcaaggctcttcattgactacaagatatcctgatacgtaatcacagATGTTTATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTCCAGCTAGCAAAGGAAAAAGCTCCCTGTATCATCTTCATTGATGAAGTAGATGCAATTG
|| ||| || || | | ||| | | || || || | || | | | | |||| ||| | || || | | ||| ||| ||| | | ||||||||||||| ||||| ||||| ||||| |||| || |||||||| || || || |||||||| ||||| || || |||||||| ||||||| ||||
-----------------------------------------------------agacattgcattaccatggaaaatatgttttattct-gatgttatcttgagcacactttatattttcaagtatgatagt-aacgatgttc-ttg-------------ctggttc--------agATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTG
upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G173849_T01 (Zea mays), 3'ss of exon 1
gtgatttcttggttttacttgtttatctatggactctcgtcagttctggtttaggatgttgttttgccttaacgcctttgtcatttacttaatttttccatgggtggagtcatcttgttcatttatcctggtcaaggctcttca-ttgactacaagatatcctgatacgtaatcacagATGTTTATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTCCAGCTAGCAAAGGAAAAAGCTCCCTGTATCATCTTCATTGATGAAGTAGATGCAATTG
|| | | | | || |||||| | | || ||| | | | | | | | | | | | || | || | | | | | |||||||||||||| ||||| ||||| ||||| |||| || |||||||| || || || |||||||| ||||| || || |||||||| ||||||| || |
------------------------------------------------------------------------cgacaaaatggag-atattgcattaccatgga-aaatctgttttattc--tgagcatactttatattttgaagtagggtagtaacgatgttcttgc-tggtt-cagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATCG
upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 5
gtgatttcttggttttacttgtttatctatggactctcgtcagttctggtttaggatgttgttttgccttaacgcctttgtcatttacttaatttttccatgggtggagtcatcttgttcatttatcctggtcaa--ggctcttcattgactacaagatatcctgatacgtaatcacagATGTTTATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTCCAGCTAGCAAAGGAAAAAGCTCCCTGTATCATCTTCATTGATGAAGTAGATGCAATTG
| || | || || | || || || | || | | ||| || | | | || | || ||| | | || |||| | | | ||||||||| ||||||||||| ||||||||||| | ||||| || || |||||||| ||||| | || || || || || || |||||| | ||||||||||
-----------------------------------------------------------------------------gtttcctctatttcacttgcacactaatgcctttattgtttatattcatacctcttgactgggttttgattaga-atgatctaacctgtaattttgt-acagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG
upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 6
gtgatttcttggttttacttgtttatctatggactctcgtcagttctggtttaggatgttgttttgccttaacgcctttgtcatttacttaatttttccatgggtggagtca-tcttgttcatttatcctggtcaaggctcttcattgactacaagatatcctgatacgtaatcacagATGTTTATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTCCAGCTAGCAAAGGAAAAAGCTCCCTGTATCATCTTCATTGATGAAGTAGATGCAATTG
|| || | | | | |||||| | || | | || ||||||||| | | | || ||| || | | | || | | |||||||| || || ||||||||||||||||| | || || |||||||| ||||| || ||| | || |||||||| |||||||||||| | ||||| ||||
-------------------------------------------------------------------attggttccaattgtaaaagttgtgactgtccatgagaattgttactatttgccatttatccatatgacaaca-ttaattatctgc------ttgtaatgcatc----cagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatcctggtcaaggctcttcattgactacaagatatcctgatacgtaatcacagATGTTTATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTCCAGCTAGCAAAGGAAAAAGCTCCCTGTATCATCTTCATTGATGAAGTAGATGCAATTG
tcctgat putative branch site (score: 3)
aagatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatttcttggttttacttgtttatctatggactctcgtcagttctggtttaggatgttgttttgccttaacgcctttgtcatttacttaatttttccatgggtggagtcatcttgttcatttatcctggtcaaggctcttcattgactacaagatatcctgatacgtaatcacagATGTTTATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTCCAGCTAGCAAAGGAAAAAGCTCCCTGTATCATCTTCATTGATGAAGTAGATGCAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA