Sequence
atgc intronic sequence ATGC exonic sequence...ttctagatacagttcaggtgtataattatgtccaatcccttgttcttggccttgcatttatagtaatggtcatgattgttcaaactgggtaatcttgcagGTTTGTGAAAGACTAGGACCGAGCTTATACGATTTCCTTCGAAAAAACAATTATCGACCATTTTCTGCAGATCTCGTTCGCGACTTTGGCCGCCAGCTGT
Basic information
species | Physcomitrella patens |
transcript | PP1S100_121V6.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S100_121V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA17G13440.2 (Glycine max), 3'ss of exon 4
ttctagatacagttcaggtgtataatt-atgtccaatcccttgttcttggccttgcatttatagtaatggtcatgat--tgttcaaactgggtaatcttg-cagGTTTGTGAAAGACTAGGACCGAGCTTATACGATTTCCTTCGAAAAAACAATTATCGACCATTTTCTGCAGATCTCGTTCGCGACTTTGGCCGCCAGCTGT
| || | ||||| || | | || || || || || | ||| | || | || | | | || ||||| | ||| | ||| ||||| |||||||||||||| ||||| |||||||||||||| ||||| | ||||| || || || ||||| | || || |
-------------gtaagtatttaatttgtgatggaatcatt--tccccaatttacaaataatttgggggttaagacaacagtgaatttaaatggttttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTAT
upper sequence: PP1S100_121V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA05G02740.3 (Glycine max), 3'ss of exon 4
ttctagatacagttcaggtgtataatt-atgtccaatcccttgttcttggccttgcatttatagtaatggtcatgat--tgttcaaactgggtaatcttg-cagGTTTGTGAAAGACTAGGACCGAGCTTATACGATTTCCTTCGAAAAAACAATTATCGACCATTTTCTGCAGATCTCGTTCGCGACTTTGGCCGCCAGCTGT
| || | ||||| || | | || || || || || | ||| | || | | || | | | || ||||| | ||| | ||| ||||| |||||||||||||| ||||| |||||||||||||| ||||| | ||||| || || || ||||| || || |
-------------gtaagtatttaatttgtgatggaatcatt--tccccaatttacaaataatttgggggttaagacaacggtgaatttaaatggttttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAAACAACTAT
upper sequence: PP1S100_121V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 4
ttctagatacagttcaggtgtataatt-atgtccaatcccttgttcttggccttgcatttatagtaatggtcatgattg--ttcaaactgggtaatcttgcagGTTTGTGAAAGACTAGGACCGAGCTTATACGATTTCCTTCGAAAAAACAATTATCGACCATTTTCTGCAGATCTCGTTCGCGACTTTGGCCGCCAGCTGT
| || | | ||| || | || ||| | | || || ||| | ||| | | || |||||| ||| | ||||| | ||| | ||| ||||| |||||||||||||| ||||| ||||||| |||||| ||||| | ||||| || || || ||||| | || ||||
-------------gtaagtatttgattgatttgtgatggattgatttc--cccaatatacataatgggggttaagggtgaattcaaa-tggttg---caacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAGTTATCGTTCATTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTGT
upper sequence: PP1S100_121V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA19G35800.1 (Glycine max), 3'ss of exon 3
ttctagataca-gttcaggtgtataattatgtccaatcccttgttcttggccttgcatttatagtaatggtcatgattgttcaaactgggtaatcttg-cagGTTTGTGAAAGACTAGGACCGAGCTTATACGATTTCCTTCGAAAAAACAATTATCGACCATTTTCTGCAGATCTCGTTCGCGACTTTGGCCGCCAGCTGT
|| || || | | | ||||| || || | || | ||| | | | || | | | | | | | | ||||| | ||| | || ||||| |||||||||||||| || || |||||||||||||| | || || ||||| ||||| || |||||| | || || |
--gtaagtatttattgatatttgtaatt-tgattaaatgaaggaatgtgcattatcatgcgagttgaaaaacttg-tggatggatttaaatggtttcaacagGTATTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAATTATCGTTCTTTATCAATTGATCTTGTTCGGGAGTTTGGCAGACAACTTT
upper sequence: PP1S100_121V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 4
ttctagatacagttcaggtgtataatt-atgtccaatcccttgttcttggccttgcatttatagtaatggtcatgattg--ttcaaactgggtaatcttgcagGTTTGTGAAAGACTAGGACCGAGCTTATACGATTTCCTTCGAAAAAACAATTATCGACCATTTTCTGCAGATCTCGTTCGCGACTTTGGCCGCCAGCTGT
| || | | ||| || | || ||| | | || || ||| | ||| | | || |||||| ||| | ||||| | ||| | ||| ||||| |||||||||||||| ||||| ||||||| |||||| ||||| | ||||| || || || ||||| | || || |
-------------gtaagtatttgattgatttgtgatggattgatttc--cccaatatacataatgggggttaagggtgaattcaaa-tggttg---caacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAGTTATCGTTCATTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTAT
upper sequence: PP1S100_121V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 4
ttctagatacagttcaggtgtataat-tatgtccaatcccttgttcttggccttgcatttatagtaatggtcatgattg--ttcaaactgggtaatcttgcagGTTTGTGAAAGACTAGGACCGAGCTTATACGATTTCCTTCGAAAAAACAATTATCGACCATTTTCTGCAGATCTCGTTCGCGACTTTGGCCGCCAGCTGT
| || ||| || | | | || | | | | || | | | || | || | | | || || | ||| ||| | | ||||| | ||| | || ||| |||| ||||||||||| ||||| |||||||||||||| | ||| | ||||| || || || ||||| | || || |
gtaagtatttagt-caattttgtgatgtctatgattttccccggtttgggaaata-gttggggttgaattttgtggatgaacttaaaatggttg---ctacagGTATTTGAGAAGCTTGGATCGAGTTTATACGATTTTCTTCGGAAAAACAATTATCGCTCCTTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTCT
upper sequence: PP1S100_121V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 5
ttctagatacagttcaggtgtataattatgtccaatcccttgttcttggccttgcatttatagtaatggtcatgattgttcaaactgggtaatcttg-cagGTTTGTGAAAGACTAGGACCGAGCTTATACGATTTCCTTCGAAAAAACAATTATCGACCATTTTCTGCAGATCTCGTTCGCGACTTTGGCCGCCAGCTGT
|| || | | | | || || || | |||| | | | |||| | | | || | || | | |||| ||||| | ||| | || ||||| |||||||||||||| ||||| |||||||||||||| ||||| | | ||||| || ||||| ||||| | || ||||
--gtaagtatatgactgatttacgatgatatgatttccccaacttcatgaat---attttggggcttaaaacttgttagtgaatttaaatggtcttaacagGTATTTGAGATGCTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCAGTTGATCTAGTCCGCGAGATTGGCAGACAACTGT
upper sequence: PP1S100_121V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 5
ttctagatacagttcaggtgtataattatgtccaatcccttgttcttggccttgcatttatagtaatggtcatgattgttcaaactgggtaatcttg-cagGTTTGTGAAAGACTAGGACCGAGCTTATACGATTTCCTTCGAAAAAACAATTATCGACCATTTTCTGCAGATCTCGTTCGCGACTTTGGCCGCCAGCTGT
|| || | | ||| || | | | || | | | || || | | || | | | || | | | ||||| | ||| | || ||||| |||||||||||||| || || |||||||||||||| ||||| | ||||| || || || ||||| | || ||||
--gtaagtataaaattgaattatgatggc-ttgatttccccaatttcacgaatattttgggggttaagactttg-tggatgaattcaaatggtttcaacagGTGTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTACGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggccttgcatttatagtaatggtcatgattgttcaaactgggtaatcttgcagGTTTGTGAAAGACTAGGACCGAGCTTATACGATTTCCTTCGAAAAAACAATTATCGACCATTTTCTGCAGATCTCGTTCGCGACTTTGGCCGCCAGCTGT
atttatagtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctagatacagttcaggtgtataattatgtccaatcccttgttcttggccttgcatttatagtaatggtcatgattgttcaaactgggtaatcttgcagGTTTGTGAAAGACTAGGACCGAGCTTATACGATTTCCTTCGAAAAAACAATTATCGACCATTTTCTGCAGATCTCGTTCGCGACTTTGGCCGCCAGCTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG