Sequence
atgc intronic sequence ATGC exonic sequencegtatgtggcgttccacacactgtttcgaacggtaaatgtttctgtttattgtctgaatggccacatgcctattcctaatgtggttaccgacagcacaagtgttttttggatatcagGTTGGAGATTTTGGACTTGCAAGATGGCAACCAGATGGACATTGTGGTGTGGAGACCAGGGTTATTGGCACCTTCGG
Basic information
species | Physcomitrella patens |
transcript | PP1S59_359V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S59_359V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA05G36280.1 (Glycine max), 3'ss of exon 5
------------------------------------------gtatgtggcg-ttccacacactgtttcgaacggtaaat-gtttctgttta--------ttgtctgaatggccacatgcctattcctaa---tgtggttac---cgacagcac-aagtgttttt-tggatatcagGTTGGAGATTTTGGACTTGCAAGATGGCAACCAGATGGACATTGTGGTGTGGAGACCAGGGTTATTGGCACCTTCGG
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gtacgtctcattcttcaatttcaaaaatggactaatgagtgttcacataatggtttcatatgctgtttagagcaattacttacttctgtttaaagattgcttatctatgaagccatatgttcataactatgcttttaggtatgttttataatatgaaatgtcttaattaattttagGTAGGAGATTTTGGACTAGCAAGGTGGCAGCCAGATGGAGACATGGGTGTGGAAACCAGGGTGATAGGAACATTTGG
upper sequence: PP1S59_359V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA08G03340.2 (Glycine max), 3'ss of exon 4
--------------------------------------------gtatgtggcgttccacacactgtttcgaacggtaaat-gtttctgttt----attg---tctgaatggccacatgcctattcctaa---tgtggttac---cgacagcac-aagtgttttttg-gatatcagGTTGGAGATTTTGGACTTGCAAGATGGCAACCAGATGGACATTGTGGTGTGGAGACCAGGGTTATTGGCACCTTCGG
|| ||| || | || | | | | | | | |||||||| |||| ||| || | ||| || ||| | | | || || | | || ||| | || | |||| |||||||||||||| ||||| ||||| ||||||||| | |||||||| |||||||| || || || || ||
gtacgtcttattcttcaatttcaaaaatggactgatgagtgttcacattaatggtttcatatgctttatacagcaatgacttacttctgtttgaagattgctttctatgaagcaatatgttcataactatgcttttaggtatgtttgaaaatatgaaatgtctcaaataattttagGTAGGAGATTTTGGACTAGCAAGGTGGCAGCCAGATGGAGACATGGGTGTGGAAACCAGGGTCATAGGAACATTTGG
upper sequence: PP1S59_359V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT3G13690.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgtggcgttccacacactgtttcgaacggtaaatgtttctgtttattgtctgaatggccacatgcctattcctaatgtggttaccgacagcacaagtgttttttggat-atcagGTTGGAGATTTTGGACTTGCAAGATGGCAACCAGATGGACATTGTGGTGTGGAGACCAGGGTTATTGGCACCTTCGG
| | | || | | || || || | | | | | || | ||| || | | | | || | || ||||||||||||||||||| || ||||||||||| || ||||| | ||||| || || | || || || ||||||||
-------------------gtatgtataaatatggtcttgctcattcatcgtaacagcagatatccac-tgtttcatatgctttttcgtcctgagtcaactttgataatatcatcagGTTGGAGATTTTGGTCTAGCAAGATGGCAGCCTGATGGGGAAATGGGTGTAGATACACGAGTGATAGGAACCTTCGG
upper sequence: PP1S59_359V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv11s0016g02430.t01 (Vitis vinifera), 3'ss of exon 5
---gtatgtggcgttccacacactgtttcgaacggtaaatgtttctgtttattgtctgaatggccacatgcctattcctaatgtggttaccgacagcacaagtgttttttggatatcagGTTGGAGATTTTGGACTTGCAAGATGGCAACCAGATGGACATTGTGGTGTGGAGACCAGGGTTATTGGCACCTTCGG
| |||| | || | | |||| | ||||| || |||||| | | | || || | | || | | |||| | |||||||||||||||||||| ||||| ||||| ||||||||| | || ||||| || | | ||||| || || ||
aacctctgtgtgtctgtgcaaaggatcatgaaccatgtgcctttctcttgcttgtctctaaagg-atgtgtgggatctaacttcggcccctg-----------gtttct-------cagGTTGGAGATTTTGGACTGGCAAGGTGGCAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGG
upper sequence: PP1S59_359V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ05818 (Selaginella moellendorffii), 3'ss of exon 6
gtatgtggcgttccacacactgtttcgaacggtaaatgtttctgtttattgtctgaatggccacatgcctattcctaatgtggttaccgacagcacaagtgttttttggatatcagGTTGGAGATTTTGGACTTGCAAGATGGCAACCAGATGGACATTGTGGTGTGGAGACCAGGGTTATTGGCACCTTCGG
| | | | || || |||| || | |||||||| |||||||| || || |||||||||||||||||| | ||| || || ||| | |||||||||||||||||
----------------------------------------------------------------gtaagttgcattgttatgaaagagcacgcgtgaagttccggttttgttccagGTTGGTGATTTTGGTCTAGCTAGATGGCAACCAGATGGAGAACTTGGAGTTGAAACCCGCGTTATTGGCACCTTCGG
upper sequence: PP1S59_359V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ12405 (Selaginella moellendorffii), 3'ss of exon 5
gtatgtggcgttccacacactgtttcgaacggtaaatgtttctgtttattgtctgaatggccacatgcctattcctaatgtggttaccgacagcacaagtg--ttttttggatatcagGTTGGAGATTTTGGACTTGCAAGATGGCAACCAGATGGACATTGTGGTGTGGAGACCAGGGTTATTGGCACCTTCGG
| | | | | | || ||| | | | || || | | | || | || ||||||| ||||||||||||||||||||||||||||| ||||| | || || ||||| || || |||||| | |||||
------------------------------------------------------gtaagttcttgtctcagtttcta-ttcgatag--gatagtccgactcacttgtctgagcatcagGTGGGAGATTTTGGACTTGCAAGATGGCAACCCAATGGAGAACTCGGAGTAGAGACAAGAGTCATTGGCGCTTTCGG
upper sequence: PP1S59_359V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ34463 (Selaginella moellendorffii), 3'ss of exon 6
gtatgtggcgttccacacactgtttcgaacggtaaatgtttctgtttattgtctgaatggccacatgcctattcctaatgtggttaccgac-agcacaagtgttttttggatat-----cagGTTGGAGATTTTGGACTTGCAAGATGGCAACCAGATGGACATTGTGGTGTGGAGACCAGGGTTATTGGCACCTTCGG
| | | | |||| | ||||| ||| | || | | | |||||||| |||||||| || || |||||||||||||||||| | ||| || || ||| | |||||||||||||||||
----------------------------------------------------------------------gtaagttacattgttatgaaagagcacgcgtgatgttccggttttgttccagGTTGGTGATTTTGGTCTAGCTAGATGGCAACCAGATGGAGAACTTGGAGTTGAAACCCGCGTTATTGGCACCTTCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacatgcctattcctaatgtggttaccgacagcacaagtgttttttggatatcagGTTGGAGATTTTGGACTTGCAAGATGGCAACCAGATGGACATTGTGGTGTGGAGACCAGGGTTATTGGCACCTTCGG
tcctaat putative branch site (score: 2)
tgtttttt putative PPT
tgtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtggcgttccacacactgtttcgaacggtaaatgtttctgtttattgtctgaatggccacatgcctattcctaatgtggttaccgacagcacaagtgttttttggatatcagGTTGGAGATTTTGGACTTGCAAGATGGCAACCAGATGGACATTGTGGTGTGGAGACCAGGGTTATTGGCACCTTCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA