Sequence
atgc intronic sequence ATGC exonic sequence...cctccactccagaacgcttgaacagtgagaagatcagtcatcaggtagcagaaaatgaatatctgaatctacgatgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG
Basic information
| species | Physcomitrella patens |
| transcript | PP1S220_67V6.1 |
| intron # | 4 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os03g06930.1 (Oryza sativa), 3'ss of exon 5
cctccactccagaacgcttgaacagtgagaagatcagtca--tcaggtagcagaaaatgaatatctgaat-ctacgatgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG-
| | ||||| || ||| || | | | | |||| || | |||| | | | | |||| || || | || |||| || || |||||||||||||| || || |||||||||||||||||| | |||||||||||| ||||| | | | |||| || |
--gtgagattgagctccatgaact-cgacgctctcatgcaaagctgatggattcaaatcaagaagagaattccatggttttttttttctttttttacg--tagGTATCGAACTGGTTCATCAACGCGCGCGTGCGGCTGTGGAAGCCAATGATCGAGGAGATGTACAAGGAGGAGTTCGGCGCGGAGA-TGGACTCCAACTCGT
upper sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os12g06340.2 (Oryza sativa), 3'ss of exon 4
cctccactccagaacgcttgaacagtgagaagatcagtcatcaggtagcagaaaatgaatatctgaatctacg-atgttttgttgacttgcatgcga--gcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG
| | | || || | | | ||| || |||||| |||||| || || | | | |||| || || |||||||||||||| | || ||||||||||||||||||| ||||||||||||| ||||| || | | | || | |
----------------------------gtacgtacgt-atacgtctacgtacaata-----ctacgtctacgtatgtttgaagtacgtgtacgtatttgtagGTGTCGAACTGGTTCATCAACGCGAGGGTGAGGCTGTGGAAGCCAATGGTGGAGGAGATGTACGCCGAGGAGACCAAGGCCAAGGAGGAGGAGGAGGAGG
upper sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os11g06020.1 (Oryza sativa), 3'ss of exon 4
-------------------------cctccactcca--gaacgcttgaacagtgagaagatca-gtcatcaggtagcagaaaatgaatatctgaatctacgatgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG
| ||| || | ||| ||| | || || | | || || | | | | | || |||| || | | || |||||||| || ||||||||||| || | || ||||||||||||| ||||| |||||||||||| | ||||| || || | || | |
gtcagaattaagatggagtttaatttttttactgtgttgattgattggtttttgattttactgcgtgttcttcttggttgaattgggtgttgaattttgtga-attttatt--ttggtttgatttcagGTTTCGAACTGGTTCATCAATGCCAGGGTGAGGCTGTGGAAGCCGATGGTGGAGGAGATGTACCTGGAGGAGACCAAGGACCAGGACGGCGGCGGCGGCG
upper sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G458728_T07 (Zea mays), 3'ss of exon 4
----------cctccactccagaacgcttgaacagtgagaagatcagtcatcaggtagcagaaaatgaatatctgaatctacgatgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGA---GTACCCTGGAGATCATACTG
| | || ||| | | |||| | || | | || | || | ||| ||| || | | | |||| || |||||||||||||| || | || |||||||||||||| ||||| |||||||||||| | ||||| ||| || | || ||||||
gtcggtaaagctgtgaatctttctttctttcttatcctgcgaatcaatttgactgttttactggcttcttaaattaacttccgaaaaaa-attg--ttcctttctgttagGTGTCCAATTGGTTCATCAATGCGAGGGTGCGGCTGTGGAAGCCTATGGTGGAGGAGATGTACCTGGAGGAGACAAAGGACCAGGACGCTGGAGGCGGCG---
upper sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G004641_T05 (Zea mays), 3'ss of exon 3
------------------cctccactccagaacgcttgaacag--------tgag--aagatcagtcatcaggtagcagaaaatgaatatctgaatctacg---atgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG--
| ||| | |||| || | || | || | | | | || | | || |||| | | || || | | | |||||| || || |||||||||||||| || || || ||||||||||| ||| | |||||||||||| || || | | | | || |||
gtgagctgattaagggattcgtcacgcacgaactgatgggtcgatctccttcgatctacgacatggccatggatggcccttggtccgtccttgctaatacggataagagctgctgcgtgggttttatgcagGTGTCCAACTGGTTCATCAACGCGCGCGTTCGACTGTGGAAGCCGATGATCGAGGAGATGTACAGGGAAGAGTTCGGGGCGGAGAT--GGACTCGCACTCGT
upper sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G148098_T01 (Zea mays), 3'ss of exon 4
cctccactccagaacgcttgaacagtgagaagatcagtcatcaggtagcagaaaatgaatatctgaatctacgatgttttgttga-cttgcatgcgagc------agGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGA-ACAAAAAGAGTACCCTGGAGATCATACTG
||| || | ||| | | ||| | | || | |||||| ||| | ||| ||| | | || | || | | || |||| |||||||||||||| || || || |||||||||||||||||| | || || |||||| ||| || | | | | || |||
---ttactggtgatctgatgatttcctgtcattttagtagtttg-tattctgtattgaataatagaa---aagatatttactgaaactcgtgtgtgttctgttctagATTTCAAATTGGTTCATCAATGCCCGTGTCCGGCTGTGGAAGCCAATGATCGAAGACATGTACAAAGAAGAGATAGGTGAGGCAGAGCTAGACTCCAACT-
upper sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA02G35450.1 (Glycine max), 3'ss of exon 5
-----cctccactccagaacgcttgaacagtgagaagatcagtcatcaggtagcagaaaatgaatatctgaatctacgatgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG
|| | || | | ||| | || | || || | | | || | || ||| | || | | | | || |||||||| ||||||||||| || || ||||| ||||| |||||||||||||| ||||| |||||| | ||||| ||||| | | || | |||
tacactcttaattcattattgtcagaattctattaaaacttgtttgca--ttcctggttataa---catggatcatgcaaacaatgaatattggtaatggaacagGTTTCAAATTGGTTCATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGATCATGAACTAAATGGTTCTG
upper sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA03G36070.1 (Glycine max), 3'ss of exon 5
cctccactccagaacgcttgaacagtgagaagatcagtcatcaggtagcagaaaatgaatatctgaatctacgatgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG
| ||| | | | | || | | | | |||| | | | | |||||| |||| || || |||||| |||||||| || || || ||||| ||||| |||||||||||||| ||||| |||||| ||||| || || | ||| |||
-------------gtaactaaactaatggtatttgactctttcatttg--gtgaatggttcttcctcttaataatgttt-gttgtgttaca--------gGTTTCAAATTGGTTTATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACACGGAGGAGATGAAGGATCATGAACAGAATCGGTCTG
upper sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA19G38690.1 (Glycine max), 3'ss of exon 7
cctccactccagaacgcttgaacagtgagaagatcagtcatcaggtagcagaaaatgaatatctgaatctacgatgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG
|| || ||| || || | | | | | || || ||| | | | || | | || || |||||||| |||||||| || || || ||||| ||||| |||||||||||||| ||||| |||||| | ||||| || || | || |||
------------gtaactagactgatgaagtaat-ggtacttgact--ctttcatttgatgaatggttcttcctcttaataatgtttggtgtgtga-cagGTTTCAAATTGGTTTATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACATGGAGGAGATGAAGGATCATGAACAGAATGGATCTG
upper sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA10G10040.1 (Glycine max), 3'ss of exon 5
----cctccactccagaacgcttgaacagtgagaagatcagtcatcaggtagcagaaaatgaatatctgaatctacgatgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG
| || || | | || | | | ||| | | | | | | |||| || | | | | | | | | || |||||||| ||||||||||| || || |||| ||||| |||||||||||||| ||||| |||||| | ||||| |||||| | | || | |||
gtaatacactcttcattattgtcaaaaatttattagaac--ttgtttgcaatcctggttatgatat-tggtcatgcta-acaacgaatattggtaatggaacagGTTTCAAATTGGTTCATTAATGCTAGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGAGCATGAACTAAATGGTTCTG
upper sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA04G03160.1 (Glycine max), 3'ss of exon 5
----cctccactccagaacgcttgaacagtgagaagatcagtcatcaggtagcagaaaatgaatatctgaatctacgatgt-tttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG
| |||| ||| ||| || | | | | || | ||| || | | | ||| ||| ||| |||| | ||||| || ||||||||||| || |||||||||||||| ||||| |||||| |||| || |||||| |||||| ||||| ||| ||| |
gtaattccttatccaaaacat---aacggtttcctagttctt--ttaactatgatgtgatggtcatgttggt----ggtgtctttattg--ttgctt-----cagGTCTCAAATTGGTTCATAAATGCACGAGTACGGCTATGGAAACCAATGATAGAAGAAATGTACAAAGAGGAGTTTGGAGAGTTTTCTGAAGACTCCAACC
upper sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA11G18270.1 (Glycine max), 3'ss of exon 3
cctccactccagaacgcttgaacagtgagaagatcagtcatca-ggtagcagaaaatgaatatctgaa-tctacgatg-ttttgttgactt-gcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG
| | ||| || || || | | | | || |||| ||| | | || || | ||||| | | | | ||||| ||||| ||||| || || || ||||| ||||| ||||||||||||||||| || |||||| | || || |||| | | || || ||
---ttgtatctaagt-tttgttttctggaaatattaaaaaaaatgaaaggtatgaatggctatggaaggtttaagacgacattgttaattaagttcataatcagGTGTCTAACTGGTTTATAAATGCCCGAGTTCGGCTATGGAAGCCAATGGTAGAAGAAATGTACTTGGAAGAGGTAAAACAAGAACCAAACAATAGCTCTC
upper sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA12G10030.1 (Glycine max), 3'ss of exon 5
--cctccactccagaacgcttgaacagtgagaagat-cagtcatcaggtagcagaaaatgaatatctgaa-tctacgatgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG
| | || | | ||| || || ||| || || || |||| ||| | | || || || | | | || | ||||| ||||| ||||| || || || ||||| ||||| ||||||||||||||||| || |||||| | || || |||| | | || || |
gaattgtatataagttttgcggtcctttgacaatattcagaaat--ggaagttatgaatggttatggaaggtttatgacatt--gataagtttattatatacagGTATCTAACTGGTTTATAAATGCCCGAGTTCGGCTATGGAAGCCAATGGTAGAAGAAATGTACTTGGAAGAGGTAAAACAAGAGCCAAACAATAGCTCCC
upper sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA06G03210.1 (Glycine max), 3'ss of exon 3
cctccactccagaacgcttgaacagtgagaagatcagtcatcaggtagcagaaaatgaatatctgaatctacgatgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG
| | ||| | | || | | || | || || | | || | | | | ||| || || | | ||| ||||| || ||||||||||| || || ||||||||||| ||||| |||||| |||| || |||||| |||||| ||||| ||| ||| |
-gtaaattccttatc---caaatcttaaccgtttccttgttcttttaactatgatgtgatggccatgttgatggtgtcttatttattgttttgctt-cagGTCTCAAATTGGTTCATAAATGCTCGAGTACGGCTATGGAAACCAATGATAGAAGAAATGTACAAAGAGGAGTTTGGAGAGTCTTCTGAAGACTCCAACC
upper sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA04G03150.1 (Glycine max), 3'ss of exon 5
-----------------------------------cctccactccagaacgcttgaacagtgagaagatcagtcatcaggta-gcagaaaatgaatatctgaatctacgatgttttgttga--cttgca----tgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG
| | | || | || || | | | |||| | || || | | | || | | || ||| ||||| | | || || | ||||| | |||||||||||||| ||| | || || || |||||||||||||| ||||| |||||| ||||||
gtacattcttaaaaactgtttccattagaaactttgtttcctgcttaaatgttttaa---ttaaactgacagtgacaagctaagtttcagctctgtaccatggttgttaatattt-gttgagGCATTCAATGTTGATATCAGGTGGCAAATTGGTTCATCAATGCAAGGGTGCGTCTCTGGAAGCCAATGGTTGAGGAAATGTACAAAGAGGA-----------------------------
upper sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA06G03200.1 (Glycine max), 3'ss of exon 4
--------------------------------------cctccactccagaacgcttgaacagtgagaagatcagtcatcaggtagcagaaa-atgaatatctgaatctacgatgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG
| ||| | || ||| ||| ||| | ||| || | | |||| | | ||| | |||| || | | | || | ||||| | |||||||||||||| ||| | || || || |||||||||||||| ||||| |||||| |||||| ||| | | | |
gtacattgttaaaaacctagaattatgagctattgagattttgtttcctgtttaattaaac--tgacaagctaagtttcagttcagtaccatcatgattgtt--aatatttgatgaggaattcaatgg--tgatatcagGTGGCCAATTGGTTCATCAATGCAAGGGTGCGTCTCTGGAAGCCAATGGTTGAGGAAATGTACAAAGAGGAGTTTGGAGACTCCGAGATGAACTGCAACC
upper sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT4G34610.2 (Arabidopsis thaliana), 3'ss of exon 4
cctccactccagaacgcttgaacagtgagaagatcagtcatcaggtagcagaaaatgaatatctgaatctacgatgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACC-CTGGAGATCATACTG
| ||| | || | | |||||| | | || | || | | | | | ||| | || | || || | ||||||| || |||||||| || |||||||| || | |||||||||||||| |||||||| ||| |||||| | |||| | | | || | |
------gtaaggaatgtttta----tttgaagattgtttctttctcttcatagtatagtttatttattgattgttgtgtgtttta--tgtttgtaaa-agGTTTCAAACTGGTTCATAAATGCACGAGTGCGTTTATGGAAGCCAATGGTGGAGGAGATATACAAGGAGGAATTCACAGAGAATGATTCCAACTCGTCTT- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagcagaaaatgaatatctgaatctacgatgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG
tgttgac putative branch site (score: 3)
aaaatgaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctccactccagaacgcttgaacagtgagaagatcagtcatcaggtagcagaaaatgaatatctgaatctacgatgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
