Sequence
atgc intronic sequence ATGC exonic sequence...tgtctcatgtgacctgtccgtagtgaactttatggattgtgggaggaatttatggtttcagtttgtgctaatattcacgagaggtcgcattttcttttagGGCTTGCGAGATGCGGCAAAAGCTGTAGATTACGGTGGACAAACTATCTTAGGCCTGACATCAAGCGAGGACGATTTTCGCACGAGGAGGACCAGAAGAT
Basic information
species | Physcomitrella patens |
transcript | PP1S106_216V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S106_216V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G031323_T01 (Zea mays), 3'ss of exon 1
tgtctcatgtgacctgtccgtagtgaactttatggattgtgggaggaatt--tatggtttcagtttgtgctaatat-tcacgagaggtcgcattttctttt-------agGGCTTGCGAGATGCGGCAAAAGCTGTAGATTACGGTGGACAAACTATCTTAGGCCTGACATCAAGCGAGGACGATTTTCGCACGAGGAGGACCAGAAGAT
|| | |||| || | | | | || | ||| || | | | | || || || | ||| |||| | |||||| || | ||||| || ||||| | |||||||||| |||||||| ||||| ||||||||||| || || || || ||| ||||| ||| ||
-gtgagcgccgccctgaccccgacggaactctcgtcccatgaatcctacgcatatagtgtagacatattcatgcatctcgtgacacatcgatccttctcgtgacacacagGGCTCGCACGGTGCGGGAAGAGCTGCCGGCTACGGTGGACTAACTATCTGAGGCCGGACATCAAGCGCGGCCGCTTCTCCTTCGACGAGGAGGAGACAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatttatggtttcagtttgtgctaatattcacgagaggtcgcattttcttttagGGCTTGCGAGATGCGGCAAAAGCTGTAGATTACGGTGGACAAACTATCTTAGGCCTGACATCAAGCGAGGACGATTTTCGCACGAGGAGGACCAGAAGAT
tgctaat putative branch site (score: 2)
tcgcattttctttt putative PPT
attttctttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtctcatgtgacctgtccgtagtgaactttatggattgtgggaggaatttatggtttcagtttgtgctaatattcacgagaggtcgcattttcttttagGGCTTGCGAGATGCGGCAAAAGCTGTAGATTACGGTGGACAAACTATCTTAGGCCTGACATCAAGCGAGGACGATTTTCGCACGAGGAGGACCAGAAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA