Sequence
atgc intronic sequence ATGC exonic sequence...ccagtatccagaacgcttttgttaaacatccacttttgtcagaggggatagaattacttgcagatggcttgacagagttacgtgacttctgtgaaatcagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA
Basic information
species | Physcomitrella patens |
transcript | PP1S258_6V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S258_6V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G004641_T05 (Zea mays), 3'ss of exon 3
----------------------------ccagtatccagaacgcttttgttaaacatccacttttgtcagagggga----tagaat-tacttgc--agatggcttgacagagttacgtgacttctgtgaaatcagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA
| | | || | | || | | | | | || | | | | | ||||| | | || | | | |||| || | || ||||| || ||||||||||||||||| || |||||| | |||||||| ||| | ||||| |||||| ||| || | | | || || ||
gtgagctgattaagggattcgtcacgcacgaactgatgggtcgatctccttcgatctacgacatggccatggatggcccttggtccgtccttgctaatacggataagagctgctgcgtgggttttatg----cagGTGTCCAACTGGTTCATCAACGCGCGCGTTCGACTGTGGAAGCCGATGATCGAGGAGATGTACAGGGAAGAGTTCGGGGCGGAGATGGACTCGCACTCGT
upper sequence: PP1S258_6V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA11G18270.1 (Glycine max), 3'ss of exon 3
ccagtatccagaac--gcttttgttaaacatccacttttgtcagaggggatagaattacttgcagatggcttgacagagttacgtgacttctgt--gaaatcagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA
||||| | | ||| ||| || | | | ||| || | | | || || || | | || | || || |||||||| ||||||||||| || || || |||||||| ||||||||||||||||||| ||||||||| |||| || ||| | | | | || |||
-ttgtatctaagttttgttttctggaaatattaaaaaaaatgaaagg---tatgaatggctatggaaggtttaagacgacattgttaattaagttcataatcagGTGTCTAACTGGTTTATAAATGCCCGAGTTCGGCTATGGAAGCCAATGGTAGAAGAAATGTACTTGGAAGAGGTAAAACAAGAACCAAACAATAGCTCTC
upper sequence: PP1S258_6V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA12G10030.1 (Glycine max), 3'ss of exon 5
ccagtatccagaacgcttttgttaaacatccacttttgtcaga----ggggatagaattacttgcagatggcttgacagagttacgtgacttctgtgaaatcagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA
| | | ||||| | | || | ||||| | | || | | || || || || | | | | | | | | | ||||| ||||||||||| || || || |||||||| ||||||||||||||||||| ||||||||| |||| || ||| | | | | || ||
--gaattgtatataagttttgcggtcctttgacaatattcagaaatggaagttatgaatggttatggaaggtttatgacattgataagtttattatata--cagGTATCTAACTGGTTTATAAATGCCCGAGTTCGGCTATGGAAGCCAATGGTAGAAGAAATGTACTTGGAAGAGGTAAAACAAGAGCCAAACAATAGCTCCC
upper sequence: PP1S258_6V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA02G35450.1 (Glycine max), 3'ss of exon 5
ccagtatccagaacgcttttgttaaacatccacttttgtcagaggggatagaattacttgcag-atggcttgacagagttacgtg-acttctgtgaaatcagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA
| | | |||| | | || | | | | || | || | |||| | | | | | | | | ||||| || || |||||||| || || |||||||| | |||||||||||||| |||||||||||| ||||||| |||||| | | || ||||
tacactcttaattcattattgtcagaattctattaaaacttgtttgcattc--ctggttataacatggatcatgcaaacaatgaatattggtaatggaacagGTTTCAAATTGGTTCATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGATCATGAACTAAATGGTTCTG
upper sequence: PP1S258_6V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA13G38910.1 (Glycine max), 3'ss of exon 4
----ccagtatccagaacgcttttgttaaacatccacttttgtcagaggggatagaattacttgcagatggcttgacagagtt---acgtgacttctgtgaaatcagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA
| | | | || || ||||| ||| | || | ||| || || ||| || || | ||| | || ||||| || |||||||| ||||| || |||||||| | |||||||||||||| || ||||||||| |||| ||| || ||| | ||| | ||
taatttacacattaaagtggttcggt--aacatgaactaataacaacagttgtag-----ctagctagcaatgtgagaggtttctgatactactctttctaatgcagGTGTCAAACTGGTTTATCAATGCCCGAGTTCGGCTTTGGAAGCCAATGGTTGAAGAAATGTACTTGGAAGAAATCAAGGAGCATGAACAAGGTAATGGCT
upper sequence: PP1S258_6V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA12G31480.2 (Glycine max), 3'ss of exon 3
ccagtatccagaacgcttttgttaaacatccacttttgtcagaggggatagaattacttgcagatggc---ttgacagagttacgtgacttctgtgaaatcagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA
| | | | | ||||| | | | || ||| | ||| || | || ||| || || | ||| | | || ||||| || |||||||| ||||| || |||||||| | |||||||||||||| || ||||||||| |||| ||| || ||| | ||| | || |
-ccctggttaatatacac--attaaagtggttcggtagcatgaactaataacgacagttgtagctagcaatgtgagaggtttctgatactctttttaatgcagGTGTCAAACTGGTTTATCAATGCCCGAGTTCGGCTTTGGAAGCCAATGGTTGAAGAAATGTACTTGGAAGAAATCAAGGAGCATGAACAAGGTAATGCCT
upper sequence: PP1S258_6V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA19G38690.1 (Glycine max), 3'ss of exon 7
ccagtatccagaacgcttttgtta-aacatccacttttgtcagaggggatagaattacttgcagatggcttgacagagttacgtgacttctgtgaaatcagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA
||| | ||| | | || | | | | ||| | | || | ||| | | ||| ||| ||||| ||||| || || ||||| || || || |||||||| | |||||||||||||| |||||||||||| ||||||| ||| || | | || |||
---gtaactagactgatgaagtaatggtacttgactctttcatttgatgaatggttcttcct------cttaataatgtttggtg-----tgtga---cagGTTTCAAATTGGTTTATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACATGGAGGAGATGAAGGATCATGAACAGAATGGATCTG
upper sequence: PP1S258_6V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA10G10040.1 (Glycine max), 3'ss of exon 5
ccagtatccagaacgcttttgttaaacatccacttttgtcagaggg-gatagaattacttgcagatggcttgacagagttacgtgacttctgtgaaatcagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA
| || | | | |||| ||| || | | | | || | | | | | || | | || || ||||| || || |||||||| || || ||||||| | |||||||||||||| |||||||||||| ||||||| ||||||| | | || ||||
gtaatacactcttcattattgtcaaaaatttattagaacttgtttgcaatcctggttatgatattggtcatgctaacaacgaatattggtaatggaa-cagGTTTCAAATTGGTTCATTAATGCTAGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGAGCATGAACTAAATGGTTCTG
upper sequence: PP1S258_6V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA14G07710.1 (Glycine max), 3'ss of exon 4
ccagtatccagaacgcttttgttaaacatcca-cttttgtcagaggggatagaat-tacttgcag----atggcttgacagagttacgtgacttctgtgaaatcagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA-
| | ||||| | ||| | | | | | | || | | || || || || | || | | | | || | | |||||| | ||||||||||| || ||| | || || |||||||||||||||| |||||||||||| || ||| || | || || || ||
------gaaaatttgtttttgatggggatcaaacagtaaaaataagtgactgcctatagttttagtcctgtgacatgtttgctaatctttatttgattcatttcagGTGGCAAACTGGTTCATTAATGCAAGGGTGCGTCTATGGAAGCCAATGGTTGAGGAAATGTACAAAGAAGAATTTGGTGATT-CTGAGATGAGCAGCAATC
upper sequence: PP1S258_6V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT4G34610.2 (Arabidopsis thaliana), 3'ss of exon 4
ccagtatccagaacgcttttgttaaacatccacttttgtcagaggggatagaattacttgcagatggcttgacagagttacgtgacttctgtgaaatcagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAA--CAGAAAGAGTACTCCGAAGATCATTCTA
| ||| | ||| || || || | || |||| || || || | ||| | | | | ||| ||| ||| || ||||||||||| || |||||||| || ||||||||||||||||| ||||| || ||| ||||||| || | ||| | | | || || | |
-----gtaaggaatgttttatttgaagattgtttctttctcttc---atagtatagtttatttattgattgttgtg--tgttttatgtttgtaaaa---gGTTTCAAACTGGTTCATAAATGCACGAGTGCGTTTATGGAAGCCAATGGTGGAGGAGATATACAAGGAGGAATTCACAGAGAATGATTCCAAC-TCGTCTT-
upper sequence: PP1S258_6V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv08s0105g00230.t01 (Vitis vinifera), 3'ss of exon 11
ccagtatccagaacgcttttgttaaacatccacttttgtcagaggggatagaattacttgcagatggcttgacagagttacgtgacttctgtga-aat-cagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA
| | || | ||| | | || |||||||| || || || | ||||| ||| ||||| |||||||||||||| || || || ||||| | |||||||||||||| || ||||||||| |||||||| || || || || || ||
--------------gtgcgcgctagaatcttgggttttttg-------tgtctttgtttgcagattatgggaactctcaaccagagctttgtgataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTGGAAGAAATGTACATGGAGGAAGTCAAGGACCACGAAGAGAATGGATCAG
upper sequence: PP1S258_6V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv06s0009g00410.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------------------------------------------------ccagtatccagaacg--cttttgttaaacatccacttttgtcagaggggatagaattacttgcagatggcttgacagagttacgtgacttctgtgaaatcagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA
|| ||||| || ||| | | || | || || |||| | | | ||| | | |||| | | ||||| || ||||||||||| || || || |||||| | |||||||||||||| || ||||||||| |||||||| || || | | || |||
gtatattgtatttactggcaatggcatgcatgtttcagttcagcttgcattatggttttgtggtgggttgggatagttctcaagttccagccttgcctgttggggagtgctactgtgtgcctgaaataatttaattggattttttactttgcaaagaaacatctaactttttgcagtgcagGTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTTGAAGAAATGTACTTGGAGGAAATAAAGGATCAGGAGCACAATGGTTCCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggatagaattacttgcagatggcttgacagagttacgtgacttctgtgaaatcagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA
gcttgac putative branch site (score: 4)
cttctgt putative PPT
aattactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccagtatccagaacgcttttgttaaacatccacttttgtcagaggggatagaattacttgcagatggcttgacagagttacgtgacttctgtgaaatcagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA