Sequence
atgc intronic sequence ATGC exonic sequence...ttcctcacatgttaagccgaacttttcatcactcaatcctgtatttaatctgttcaagagattgaagtactctcatcaactttgtcatatccatccacagATTTTATTCATGCCTAGAAGTGGCTTCAGAGTACTTCAGATCTGGAGCTGACAAGATATCTATTGGAAGTGATGCTGTTTATGCTGCTGAGGAGTATCTC
Basic information
species | Physcomitrella patens |
transcript | PP1S43_232V6.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S43_232V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os03g15120.1 (Oryza sativa), 3'ss of exon 10
-ttcctcacatgttaa-gccgaacttttcatcactcaatcctgtatttaatctgttcaagagattgaagtactctcatcaactttgtcatat-ccatccacagATTTTATTCATGCCTAGAAGTGGCTTCAGAGTACTTCAGATCTGGAGCTGACAAGATATCTATTGGAAGTGATGCTGTTTATGCTGCTGAGGAGTATCTC
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ctctcccccatctttttgaggtgttatttgttgtttg--tcaatagtcaatactgagaaggaaaagga-cagacagagtaattatgtattcttcccttgtcagATACTACTCAAGTTTGGAAGTAGCGTCAGAGTACTTCAGGTCTGGTGCTGACAAGATTTCAATTGGTAGTGATGCCGTTTTTGCTGCTGAAGCCTATTTG
upper sequence: PP1S43_232V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA18G12920.1 (Glycine max), 3'ss of exon 13
--------------------------------------ttcctcacatgttaagccgaac-ttttcatcactcaatcctgtattt------aatctgttcaag-agattgaagtactctcatcaactttgtcatatccatccacagATTTTATTCATGCCTAGAAGTGGCTTCAGAGTACTTCAGATCTGGAGCTGACAAGATATCTATTGGAAGTGATGCTGTTTATGCTGCTGAGGAGTATCTC
| || ||| || || || || | ||| || | || || | | ||||| ||| | | ||| | | ||| | || | ||| | |||||| | | ||||| ||||| || ||||| || ||||| ||||| ||||| || |||||||||||||| ||||||||||| || || ||| |
gtattattattgatcattatggagattatgctattgacattcttgcatttttttccctctattgaaattattcagtcttatagttctatcaattgtgttccctcagaattttcaaatctttttgatccgatcaattatattctcagGTACTATTCAAGTTTGGAAGTTGCTTCTGAATACTTTAGGTCTGGGGCTGATAAGATTTCCATTGGAAGTGATGCAGTTTATGCTGCAGAAGAATATTTA
upper sequence: PP1S43_232V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA18G10460.1 (Glycine max), 3'ss of exon 13
--------------------------------------ttcctcacatg-ttaagccgaacttttcatcactcaatcctgta-tttaatctgtt------caagagattgaagtactctcatcaactttgtcatatccatccacagATTTTATTCATGCCTAGAAGTGGCTTCAGAGTACTTCAGATCTGGAGCTGACAAGATATCTATTGGAAGTGATGCTGTTTATGCTGCTGAGGAGTATCTC
|| || ||| || || || || | ||| || | || ||| ||| || | ||| | | ||| | | ||| | || | ||| | ||||| | | ||||| ||||| || ||||| || ||||| ||||| ||||| || |||||||||||||| ||||||||||| || || ||| |
gtattattactgatcattatggagattatgctattgactttcttgcattctttcccctctattgaaattattcagtcttatagttttatcaattgtgttccctcagaattttcaaatctttttgatccgatcaattatattctcagGTACTATTCTAGTTTGGAAGTTGCTTCTGAATACTTTAGGTCTGGGGCTGATAAGATTTCCATTGGAAGTGATGCAGTTTATGCTGCAGAAGAATATTTA
upper sequence: PP1S43_232V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv19s0090g00810.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------------------ttcctcacatgttaagccgaacttttcatcactcaat---------cctgtatttaatctgttcaa--gagattgaagtactct-----catcaacttt---gtcatatccatccacagATTTTATTCATGCCTAGAAGTGGCTTCAGAGTACTTCAGATCTGGAGCTGACAAGATATCTATTGGAAGTGATGCTGTTTATGCTGCTGAGGAGTATCTC
|| | | ||| | |||| | | | ||| ||| | | | | | || | || | |||| || | | ||| | ||| || | ||| ||| | |||||| | | ||||| |||||||| || ||||| || || || || || || ||||||||||||||||| |||||||||||||| || ||| |
gtacacacttgggtgttgttttctggatgattgtcgttcttttttaatttatttttatcttttatttttttttattaaatgttaattctccttcagtgattttcttgagatgaaagtgaactattatggatacattatattttaaaccaatctcttcctcagGTATTATTCTAGTTTGGAAGTTGCTTCAGAATATTTCAGGTCAGGGGCAGATAAAATTTCTATTGGAAGTGATGCAGTTTATGCTGCTGAAGAATATATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatctgttcaagagattgaagtactctcatcaactttgtcatatccatccacagATTTTATTCATGCCTAGAAGTGGCTTCAGAGTACTTCAGATCTGGAGCTGACAAGATATCTATTGGAAGTGATGCTGTTTATGCTGCTGAGGAGTATCTC
atttaat putative branch site (score: 4)
tccatcc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcctcacatgttaagccgaacttttcatcactcaatcctgtatttaatctgttcaagagattgaagtactctcatcaactttgtcatatccatccacagATTTTATTCATGCCTAGAAGTGGCTTCAGAGTACTTCAGATCTGGAGCTGACAAGATATCTATTGGAAGTGATGCTGTTTATGCTGCTGAGGAGTATCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - -cacatgt