Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaccattcaaactttagaaccgactcgcatcctcaaccactttcttaacttgcagttgaactggtcgggtgatttatagattgatagattccttcctgcattcctgaatatgttttccagACCTCTGGCGTAACGCACAATGGCCCCGTGTCGAGGGTTTTATACTTCACGGGAGCAACCAACATTCTCTACACCTTTGGAAGCCACGCTGTGACAGT
Basic information
species | Physcomitrella patens |
transcript | PP1S213_89V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S213_89V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 2
gtaaaaccattcaaactttagaaccgactcgcatcctcaaccactttcttaacttgcagttgaactggtcgggtgatttatagattgatagattccttcctgcattcctgaatatgttttccagACCTCTGGCGTAACGCACAATGGCCCCGTGTCGAGGGTTTTATACTTCACGGGAGCAACCAACATTCTCTACACCTTTGGAAGCCACGCTGTGACAGT
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----------------------ataagatcaaagtcccaaacgtcacttatttatgataacaaaatgatagtaatagtgatagatag-taattgtaatagtgcatatattggga-ataatgcagGTGGAGGGTGTGGCGCACTCTGGGCCCACAAGCATCGTGCTCTACTTCACGGGGGCCACCAACATCCTCTACACCTTCGGGGGCCACGCTGTCACCGT
upper sequence: PP1S213_89V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G045057_T02 (Zea mays), 3'ss of exon 4
--gtaaaaccattcaaactttagaaccgactcgcatcctcaaccactttcttaacttgcagttgaactggtcgggtgatttata-gattgatagattccttcctgcattcctgaatatgttttccagACCTCTGGCGTAACGCACAATGGCCCCGTGTCGAGGGTTTTATACTTCACGGGAGCAACCAACATTCTCTACACCTTTGGAAGCCACGCTGTGACAGT
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gtatatatgcgct-gagcgtgtgatatgatgcac-tagtcgattgatcgcctg-cttgcgctatgtccag-cagatcgtgtatatggccgtaccaaacattaattgatggacgacaatattat--agGTGGAAGGTGTGACGCACTCGGGCCCAAGCAAGATGGTGCTCTACTTCACCGGTGCCACCAACATCCTCTACACCTTTGGAGGCCATGCTGTCACTGT
upper sequence: PP1S213_89V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaaaaccattcaaactttagaaccgactcgcatcctcaaccactttct-taacttgcagttgaactggtcgggtgatttatagattgatagattccttcctgcattcctgaatatgttttccagACCTCTGGCGTAACGCACAATGGCCCCGTGTCGAGGGTTTTATACTTCACGGGAGCAACCAACATTCTCTACACCTTTGGAAGCCACGCTGTGACAGT
| ||| || || | ||| | || | ||| | || | | | ||| ||| | | || ||| ||| || | ||| || || | | || | ||| ||| || | | ||| | |||||||| ||||| ||||||||||||||||||||||| ||||||| || |||||
-------------gtcattataattaacacaaatcttgttttgattattataagatatagacatatagtcctggttatt-gttgtttaatatatttattttt-catataaaaa----------agGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT
upper sequence: PP1S213_89V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
-----------gtaaaaccattcaaactttagaaccgactcgcatcctcaaccactttcttaa-cttgcagttgaactggtcgggtgatttatagattgatagattccttcctgcattcctgaatatgttttccagACCTCTGGCGTAACGCACAATGGCCCCGTGTCGAGGGTTTTATACTTCACGGGAGCAACCAACATTCTCTACACCTTTGGAAGCCACGCTGTGACAGT
|| | | | | | || || | | | ||| | || | |||||||| ||| | || || | ||| || || ||| || || || | |||| |||||| | |||| | |||||||| || || ||||||||||||||||||||||| | || ||||| |||||
gtatgtatttaccttaattagctgtattcatcacttagttttaatttcaaataattcccataatcccatcccccctttgatacattgatttatttattaagtaatcccatgctgatttgcttg------tttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgggtgatttatagattgatagattccttcctgcattcctgaatatgttttccagACCTCTGGCGTAACGCACAATGGCCCCGTGTCGAGGGTTTTATACTTCACGGGAGCAACCAACATTCTCTACACCTTTGGAAGCCACGCTGTGACAGT
gattgat putative branch site (score: 4)
tgttttcc putative PPT
atttatagattgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaccattcaaactttagaaccgactcgcatcctcaaccactttcttaacttgcagttgaactggtcgggtgatttatagattgatagattccttcctgcattcctgaatatgttttccagACCTCTGGCGTAACGCACAATGGCCCCGTGTCGAGGGTTTTATACTTCACGGGAGCAACCAACATTCTCTACACCTTTGGAAGCCACGCTGTGACAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG