Sequence
atgc intronic sequence ATGC exonic sequence...gttgttgttatttagatccttatgttcttggttgaggtgatcgaacaggagcatggatttacgttttaattgttgtgattcgtttgactcgtatttatagGTGTTGGAAGGTCTTGTTTACTTGCACGAGCAGGGTGTCATTCACCGTGATATCAAGGGTGCCAACATACTGACCACGAAGGAG
Basic information
species | Physcomitrella patens |
transcript | PP1S131_142V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S131_142V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G017654_T02 (Zea mays), 3'ss of exon 5
gttgttgttatttagatccttatgttcttggttgaggtgatcgaacaggagcatggatttacgttttaattgttgtgattcg--tttgactcgtatttat--agGTGTTGGAAGGTCTTGTTTACTTGCACGAGCAGGGTGTCATTCACCGTGATATCAAGGGTGCCAACATACTGACCACGAAGGAG
||||||| |||| | || | | | | | |||| || || | || | ||| | ||| | | |||||||||||||||||||||| |||| || || ||||||||||| | ||||||||||| || || |||||||| || || |||
-----------------------gttcttgt----ggtggttcaatactactacttttctcttttttccttatttttatctgattttagtttttatgtgtccagGTGTTGGAAGGTCTTGTTTATCTGCATGAACAAGGTGTCATTCATAGAGATATCAAGGGCGCAAATATACTGACTACCAAAGAG
upper sequence: PP1S131_142V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G305321_T01 (Zea mays), 3'ss of exon 2
gttgttgttatttagatccttatgttcttggttgaggtgatcgaacaggagcatggatttacgttttaattgt-tgtgattcgtttgactcgtatttatagGTGTTGGAAGGTCTTGTTTACTTGCACGAGCAGGGTGTCATTCACCGTGATATCAAGGGTGCCAACATACTGACCACGAAGGAG
| ||| || | |||| || || || ||| | ||| || | | ||||| | | ||| |||||||||||||||||||||| |||| || || ||||||||||| | ||||||||||| || || ||||||| || || |||
---------------gtgcttgtggt---ggttactgtaatactactacttttctctttttccccttatttttatctgatttcagTT-TTTATATGACCAGGTGTTGGAAGGTCTTGTTTATCTGCATGAACAAGGTGTCATTCATAGAGATATCAAGGGCGCAAATATACTGAGTACCAAAGAG
upper sequence: PP1S131_142V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA11G10810.1 (Glycine max), 3'ss of exon 5
gttgttgttatttagatccttatgttcttggttgaggtgatcgaacaggagcatggatttacgttttaattgttgtgattcgtttgactcgtatttatagGTGTTGGAAGGTCTTGTTTACTTGCACGAGCAGGGTGTCATTCACCGTGATATCAAGGGTGCCAACATACTGACCACGAAGGAG
||| | | | | | | | || ||||||| | | || |||| ||||| || | | || | | |||||||||||||||| | ||||| | ||||| |||||||| || || || ||||| |||||||| |||||| |||| || || |||
------gtt-tgtgggtg-taagactattcattgaggtttttccaggatttgatttttttatattttattttatactaaatgtattatattatgagatagGTGTTGGAAGGTTTGGTTTATCTACACGAACAGGGTGTTATCCATCGGGATATTAAGGGTGCAAACATATTGACAACTAAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caggagcatggatttacgttttaattgttgtgattcgtttgactcgtatttatagGTGTTGGAAGGTCTTGTTTACTTGCACGAGCAGGGTGTCATTCACCGTGATATCAAGGGTGCCAACATACTGACCACGAAGGAG
atttacgttttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgttgttatttagatccttatgttcttggttgaggtgatcgaacaggagcatggatttacgttttaattgttgtgattcgtttgactcgtatttatagGTGTTGGAAGGTCTTGTTTACTTGCACGAGCAGGGTGTCATTCACCGTGATATCAAGGGTGCCAACATACTGACCACGAAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG