Sequence
atgc intronic sequence ATGC exonic sequencegtatgcaccaaattgcagcgattttgtcaacgtcacagtggcatattcactgaggacaaatgttagtggatagaaatagtggtggcagtaacgagtcactgatgtcgccgagtgggtgagttaaggtaagtctggttttggtattctactgagcccttgttgctgttatgtgggtgaacagTTGGAGGAACGACACCAATGTTATCCTTGCAGATGAAATGGGTCTTGGCAAGACAGTTCAGTCAGTCTCGATGCTTGGATTTTTGCAG
Basic information
species | Physcomitrella patens |
transcript | PP1S93_123V6.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S93_123V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G141258_T01 (Zea mays), 3'ss of exon 10
gtatgcaccaaattgcagcgattttgtcaacgtcacagtggcatattcactgaggacaaatgttagtggatagaaatagtggtggcagtaacgagtcactgatgtcgccgagtgggtgagttaaggtaagtctggttttggtattctactgagcccttgttgctgttatgtgggtgaacagTTGGAGGAACGACACCAATGTTATCCTTGCAGATGAAATGGGTCTTGGCAAGACAGTTCAGTCAGTCTCGATGCTTGGATTTTTGCAG
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----------------------------------------------------------------------------------------------gtacgtaagatcaatatgatctgcatatatgcacagcagaatgcaaatactctgtt---ttctgattgtt--tgactggtaacacagGTGGAGAAACGATACTAATGTTATACTTGCTGATGAAATGGGTCTGGGAAAAACTATCCAATCTGTATCCATGCTTGGCTTCCTTCAT
upper sequence: PP1S93_123V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 10
gtatgcaccaaattgcagcgattttgtcaacgtcacagtggcatattcactgaggacaaatgttagtggatagaaatagtggtggcagtaacgagtcactgatgtcgccgagtgggtgagttaaggtaagtctggttttggtattctactgagcccttgttgctgttatgtgggtgaacagTTGGAGGAACGACACCAATGTTATCCTTGCAGATGAAATGGGTCTTGGCAAGACAGTTCAGTCAGTCTCGATGCTTGGATTTTTGCAG
| || | | | | ||| | | ||| || | |||| | |||| || ||||||||| || || || ||||| || | || ||||||||||| ||||| || || ||||||||||| ||||||||||| ||| | |||
-------------------------------------------------------------------------------------------------------------gtatgcatatctgtatatttgtcaaggt---acattttaattttttggtgttctaaatctgtgtatgg-cagTTGGAGAAATGATACAAATGTCATTTTAGCTGATGAAATGGGCCTTGGAAAAACTGTTCAGTCAGTATCGATGCTTGGTTTTCTACAG
upper sequence: PP1S93_123V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatgcaccaaattgcagcgattttgtcaacgtcacagtggcatattcactgaggacaaatgttagtggatagaaatagtggtggc-agtaacgagtcactgatgtcgccgagtgggtgagttaaggtaagtctggttttggtattctactgagcccttgttgctgttatgtgggtgaacagTTGGAGGAACGACACCAATGTTATCCTTGCAGATGAAATGGGTCTTGGCAAGACAGTTCAGTCAGTCTCGATGCTTGGATTTTTGCAG
||||| | | | | || | | | | ||| | | || || | | || | | | | ||| | | | || || | || ||| ||| || || || ||||| || | || ||||||||||||||||| || || ||||||||||| || |||||||| |||||||||
-----------------------------------------------------------gtgttacttatctcacttcacaattgctgatgattatttacttgtctactcggtcttatgtgattctttacttgtcggctcggtctaatgattggcttcctttcattttc----------cagCTGGCTTAATGATACTAATGTCATTTTGGCTGATGAAATGGGTCTTGGTAAAACTGTTCAGTCAGTTTCAATGCTTGGGTTTTTGCAG
upper sequence: PP1S93_123V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 10
gtatgcaccaaattgcagcgattttgtcaacgtcacagtggcatattcactgaggacaaatgttagtggatagaaatagtggtggcagtaacgagtcactgatgtcgccgagtgggtgagttaaggtaagtctggttttggtat-tctactgagcccttgttgctgttatgtgggtgaacagTTGGAGGAACGACACCAATGTTATCCTTGCAGATGAAATGGGTCTTGGCAAGACAGTTCAGTCAGTCTCGATGCTTGGATTTTTGCAG
|| | | | | || | | | | | ||| | || | | || || ||| |||| | || | |||| | | | | || | || |||||| ||||| || || || |||||||| | || |||||||||||||||||||| || || |||||||| || |||||||| |||||||||
-------------------------------------------------------------gtatgctggtttcttttgttttag-aatgatcagtttaaactaaaaaaatgtactttaaatataatat-tctaattttagcatatatactaatcagcttct-ctttcata-----gaacagCTGGAGAAATGATACTAATGTTATTTTGGCTGATGAAATGGGTCTTGGCAAAACTGTGCAGTCAGTTTCTATGCTTGGGTTTTTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagtctggttttggtattctactgagcccttgttgctgttatgtgggtgaacagTTGGAGGAACGACACCAATGTTATCCTTGCAGATGAAATGGGTCTTGGCAAGACAGTTCAGTCAGTCTCGATGCTTGGATTTTTGCAG
tattcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcaccaaattgcagcgattttgtcaacgtcacagtggcatattcactgaggacaaatgttagtggatagaaatagtggtggcagtaacgagtcactgatgtcgccgagtgggtgagttaaggtaagtctggttttggtattctactgagcccttgttgctgttatgtgggtgaacagTTGGAGGAACGACACCAATGTTATCCTTGCAGATGAAATGGGTCTTGGCAAGACAGTTCAGTCAGTCTCGATGCTTGGATTTTTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA