Sequence
atgc intronic sequence ATGC exonic sequence...tgttttctttcttccttcttctttctacttctgcatctttccatttctttctttctctttgtgtttttattttttccttttttttttggtttcttaagagGTCTACGTCGCGCAGGTTGGAAGAGCTGCAAGTTTTGGACATCAAGTTTCTTTATGGCTGTGCTAAACCTACTATTGCAGTTCTCTATCAG
Basic information
species | Physcomitrella patens |
transcript | PP1S458_4V6.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S458_4V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 7
tgttttctttcttccttcttctttctacttctgcatctttccatttctttctttctctt-tgtgtttttattttttccttttttttttggtttcttaagagGTCTACGTCGCGCAGGTTGGAAGAGCTGCAAGTTTTGGACATCAAGTTTCTTTATGGCTGTGCTAAACCTACTATTGCAGTTCTCTATCAG
| | | | | | || ||||| || | | | || || ||| | || || | | | | || |||| | ||||| || ||||| |||||||||||||| || |||||||||| |||||||||||| | || ||||| |||
---------------atataacattaccattcgggggttaatatttcattaaggatgatgcatattcgtacatttgaccttaccagagagtaacacttgcattttctttctt-cagGCTTGAAGAACTTCAAGTATTGGACATCAAGTTCCTGTATGGCTGTGTTAAACCTACTATAGTTGTCCTCTACCAG
upper sequence: PP1S458_4V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 7
tgttttctttcttccttcttctttctacttctgcatctttccatttctttctttctctttgtgtttttattttttccttttttttttggtttcttaagagGTCTACGTCGCGCAGGTTGGAAGAGCTGCAAGTTTTGGACATCAAGTTTCTTTATGGCTGTGCTAAACCTACTATTGCAGTTCTCTATCAG
| | |||| | || | | | | | | |||| | | || | | || || | | || | | | | || ||| | ||||| || ||||| |||||||||| ||||| |||| ||||||||||||||||||| || ||||| |||
-------------cgattaactttattgggatgatgaacttcgatattctgagtaatattgtctaatagttaatgttatgttattcagactaagtagca--ttttcttctgtcagACTTGAAGAACTTCAAGTACTGGACATCAAATTTCTACATGGTTGTGCTAAACCTACTATTGTTGTCCTCTACCAG
upper sequence: PP1S458_4V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 7
tgttttctttcttccttcttctttctacttctgcatctttccatttctttctttctctttgtgtttttattttttccttttttttttggtttcttaagagGTCTACGTCGCGCAGGTTGGAAGAGCTGCAAGTTTTGGACATCAAGTTTCTTTATGGCTGTGCTAAACCTACTATTGCAGTTCTCTATCAG
||| || | | |||| | | | || |||| || ||| ||| | |||||| ||| | ||| || | | | | | | |||| | || ||||| ||||||||||| ||||||||||||||||| ||| | ||||| ||||||| |||||||| |||
-----acttaattgaatagtttttcatcctttatatgtttcttgaagttgttttatctac-tatttttagtttaacactttccttctaat---------gatgaatgcttttcagGCTTGAGGAGCTTCAAGTTTTGGATATCAAGTTTCTTTATGGATGTTCAAAACCAACTATTGTTGTTCTCTACCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttctttctctttgtgtttttattttttccttttttttttggtttcttaagagGTCTACGTCGCGCAGGTTGGAAGAGCTGCAAGTTTTGGACATCAAGTTTCTTTATGGCTGTGCTAAACCTACTATTGCAGTTCTCTATCAG
ttctctttgtgttttt CT-rich tract
tttttattttttcctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttttctttcttccttcttctttctacttctgcatctttccatttctttctttctctttgtgtttttattttttccttttttttttggtttcttaagagGTCTACGTCGCGCAGGTTGGAAGAGCTGCAAGTTTTGGACATCAAGTTTCTTTATGGCTGTGCTAAACCTACTATTGCAGTTCTCTATCAG
- - - - - - - - - - - - - - ttctgca