Sequence
atgc intronic sequence ATGC exonic sequencegtatgttcaaaaatcttctacgtcatataatggtttttgtctattcaacaaaatgtctcggctaagcgcattatttgaaatcttattcaacgttcttggtagacctgggattgggtgtatccgaatatcttgattttggttgatatcgcttagaatcaaaatgtaacgttttgtattgatgatttgcagTTCCTCCAGCATATTATGCACATCTAGCTGCTTTTCGTGCCAGGTTCTACATGGATCCAGAAGCTTCAGATACTGGTTCTGTTACTAGTGGGTTGGGAGG
Basic information
species | Physcomitrella patens |
transcript | PP1S28_182V6.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S28_182V6.1 (Physcomitrella patens), 3'ss of exon 19
lower sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 21
gtatgttcaaaaatcttctacgtcatataatggtttttgtctattcaacaaaatgtctcggctaagcgcattatttgaaatcttattcaacgttcttggtagacctgggattgggtgtatccgaatatcttgattttggttgatatcgcttagaatcaaaatgtaacgttttgtattgatgatttgcagTTCCTCCAGCATATTATGCACATCTAGCTGCTTTTCGTGCCAGGTTCTACATGGATCCAGAAGCTTCAGATACTGGTTCTGTTACTAGTGGGTTGGGAGG
||| | | || || || | |||| | || ||| ||| | | | | | | || || || ||| || || | || | || | || | | | || ||| || | ||| || || || | |||| || | |||||||||||||||||||||||||||| |||| || ||||| || | ||||| ||||| ||||| ||| | ||| |||| | || ||
gtaagcccgtgcttcaattaatatgtagtttttcggttgtttggtcccagttatgactcacccatgtccttaccctcaacactagttgaacagctatgatatttttaacat-gattgaactttaacctttatacttgtcttgg-atagtttaaaacttaattg----actggaaattgttgttatgcagTTCCTCCAGCATATTATGCACATTTAGCAGCGTTTCGAGCACGTTTCTATATGGAACCAGATATGCAAGACAATGGCTCTGCAGGTGACGGTAATGGTCA
upper sequence: PP1S28_182V6.1 (Physcomitrella patens), 3'ss of exon 19
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 20
gtatgttcaaaaatcttctacgtcatataatggtttttgtctattcaacaaaatgtctcggctaagcgcattatttgaaatcttattcaacgttcttggtagacctgggattgggtgtatccgaatatcttgattt--tggttgatatcgcttagaatcaaaa--tgtaacgttttgtattga--tgatttgcagTTCCTCCAGCATATTATGCACATCTAGCTGCTTTTCGTGCCAGGTTCTACATGGATCCAGAA--GCTTCAG-ATACTGGTTCTGTTACTAGTGGGTTGGGAGG
| | | |||| | | | | | || || || | | | |||| || | | | ||| | || | | | | || ||||||||||||||| |||||||||||| | || |||||||| || ||||||| ||||| ||||| || ||| | | ||| || | |||| |
-----------------------------------------------------------------------------------------------tgaacacaaaggggacaaagggaaacaaattactttaatgtactattctatattatctatatttgtttcttacaacttagtggacttaattcatgtgcagTTCCTCCAGCGTATTATGCACATTTGGCAGCTTTTCGAGCGCGGTTCTATATGGAGCCAGACCTGCAGCAGGAGAATGGCTCCTCAGGTGGTGGCTCCAA---
upper sequence: PP1S28_182V6.1 (Physcomitrella patens), 3'ss of exon 19
lower sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 21
gtatgttcaaaaatcttctacgtcatataatggtttttgtctattcaacaaaatgtctcggctaagcgcattatt----tgaaatcttattcaacgttcttggtagacctgggat-tgggtgta-tccgaatatcttgattttggttgatatcgcttagaatcaaaatgtaacgttttgtattgatgatttgcagTTCCTCCAGCATATTATGCACATCTAGCTGCTTTTCGTGCCAGGTTCTACATGGATCCAGAAGCTTCAGATACTGGTTCTGTTACTAGTGGGTTGGGAGG
||| | | | | | |||| || |||| | || | || | || | | | || | || || || ||| || || || ||| || | | || || ||| | || | ||| || || || | |||| || | |||||||||||||||||||||||||||| |||| || || || || | ||||| ||||| ||||| ||| | ||| |||| | ||| ||
gtaagcctg----tgcttcaattaatatgttgtttttcagttgtttggtccca-gttatgactcaccatgtccttaccctcaagactagttgaacagctatgctattttaatgacatggttgaacttttaaccctttatacttgtcttggatagtttaaaacttaattg----actggaaattgttgttgtgcagTTCCTCCAGCATATTATGCACATTTAGCAGCGTTCCGAGCACGTTTCTATATGGAGCCAGATATGCAAGACAATGGCTCTGCAGGTGATGGCAATGGTTA
upper sequence: PP1S28_182V6.1 (Physcomitrella patens), 3'ss of exon 19
lower sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 12
gtatgttcaaaaatcttctacgtcatataatggtttttgtctattcaacaaaatgtctcggctaagcgcattatttgaaatct-tattcaacgttcttggtagacctgggattgggtgtatccgaatatcttgattttggttgatatcgcttagaatcaaaatgtaacgttttgtattgatgatttgcagTTCCTCCAGCATATTATGCACATCTAGCTGCTTTTCGTGCCAGGTTCTACATGGATCCAGAA--GCTTCAG-ATACTGGTTCTGTTACTAGTGGGTTGGGAGG
||| |||| | || | | | || | | || | || | ||| | | | | || | || ||| ||| | | ||| ||| ||||||||||||||| ||||| |||||| |||| |||||||| || | ||||| ||||| ||||| || ||| | | ||| || | |||| | |
--------------------------------------------------------------------------------tctatattttatatttatat----ctttatatcatatttgtc--atgattgaggtttcagcttgttttgcaaaatat-aaatcttaatggacttcattcatg---tgcagTTCCTCCAGCGTATTACGCACATTTAGCAGCTTTTCGAGCACGTTTCTATATGGAGCCAGACCTGCAGCAGGAGAATGGCTCCTCAGGTGGTGGCTCCAG---
upper sequence: PP1S28_182V6.1 (Physcomitrella patens), 3'ss of exon 19
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 18
gtatgttcaaaaatcttctacgtcatataatggtttttgtctattcaacaaaatgtctcggctaagcgcattatttgaaatcttattcaacgttcttggtagacctgggattgggtgtatccgaatatcttgattttggttgatatcgcttagaatcaaaatgtaacgttttgtattgatgatttgcagTTCCTCCAGCATATTATGCACATCTAGCTGCTTTTCGTGCCAGGTTCTACATGGATCCAGAAGCTTCAGATACTGGTTCTGTTACTAGTGGGTTGGGAGG
| || | |||||| || | | | | || || | | |||||| | ||| | || |||| | | | || | | ||||||||||||||||||||||||||||||| |||| || ||||| ||| | ||||||||||| || || || | |||||| | |||| |
----------------------------------------------------------------------------------tcctttgaagttctttgttcaaattgtcctccttgag---gagctccatcattttgttc--tatgagctgcaactgaaat--agctaaatccatggctcatttgcagTTCCTCCAGCATATTATGCACATTTAGCAGCATTTCGAGCCCGATTCTACATGGAGCCTGACATGCAGGAGAATGGTTCAAATGGAGGTGGCAGTG---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttggttgatatcgcttagaatcaaaatgtaacgttttgtattgatgatttgcagTTCCTCCAGCATATTATGCACATCTAGCTGCTTTTCGTGCCAGGTTCTACATGGATCCAGAAGCTTCAGATACTGGTTCTGTTACTAGTGGGTTGGGAGG
tattgat putative branch site (score: 3)
aatcaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttcaaaaatcttctacgtcatataatggtttttgtctattcaacaaaatgtctcggctaagcgcattatttgaaatcttattcaacgttcttggtagacctgggattgggtgtatccgaatatcttgattttggttgatatcgcttagaatcaaaatgtaacgttttgtattgatgatttgcagTTCCTCCAGCATATTATGCACATCTAGCTGCTTTTCGTGCCAGGTTCTACATGGATCCAGAAGCTTCAGATACTGGTTCTGTTACTAGTGGGTTGGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC