Sequence
atgc intronic sequence ATGC exonic sequencegtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggacctctgctgaaattgtaaaattgaccttgacgatggtggactcttgtgcagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT
Basic information
species | Physcomitrella patens |
transcript | PP1S376_19V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S376_19V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os06g14540.1 (Oryza sativa), 3'ss of exon 1
gtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggacctctgctgaaattgtaaaattgaccttg--acgatggtggactcttgtg---cagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT
| | | | || | | || | ||| | | | ||| | | | | | | || || | | | |||| | | ||| | | | | ||||| || ||| ||||||||||||||||| || |||||||| ||||||||| | || ||||| |||| | | | |||| ||||| | | || |
------------------------------gtacggaccaccaccgctctctctctctctctgttctagcattaatgcggtttgca---atgtagtagtaatgatgacgatgtcgctgacggtttcttggaatggtggcgtggcgtggcgtggcagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGGCTGATCGACT
upper sequence: PP1S376_19V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os02g50040.1 (Oryza sativa), 3'ss of exon 1
gtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggacctctgctgaaattgtaaaattgaccttgacga---tggtggactcttgtgcagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT
| | |||| || ||| || |||| | | | || || ||| |||| | | | ||| | || || | ||| |||| || |||| ||||||||||||||||| || |||||||| ||||||||| | || ||||| |||| | | || |||| ||||| | | || |
--------------------------------------------------------gtacgtattctcgt-cctata-acttggcgtt---aagaatgtactactggtgaagcagcattgtgatttgtgagtaacctgctgtggccgcgtgtagGTGGACTTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTGATGTCGTGGGGGCTGATCGACT
upper sequence: PP1S376_19V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G455642_T02 (Zea mays), 3'ss of exon 1
gtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggac-ctctgctgaaattgtaaa-attgaccttgacgatggtggactcttgtgcagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT
|| | ||| ||| | ||||||| || | | ||| || | | | ||| | | | || | || | || || | || |||||| || ||| || ||||||||||||||||| |||||||| ||||||||| | || ||||| |||| | | | |||| ||||| | | || |
-------------------------gtctgtctctctctctctttcagtaatccctccc---attcatgcgcacaccatcctcgtatgcgtacgcacgagcgcattgcgtcagtaatgaacacgcacgcatgctctgctgtgcact---gcagGTGGACCTGACGGGCGGGTACTACGACGCGGGCGACAACGTGAAGTTCGGGTTCCCTATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
upper sequence: PP1S376_19V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G455642_T01 (Zea mays), 3'ss of exon 1
gtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggac-ctctgctgaaattgtaaa-attgaccttgacgatggtggactcttgtgcagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT
| | | | ||| | ||| ||| | ||||||| || | | ||| || | | | ||| | | | || | || | || || | || |||||| || ||| || ||||||||||||||||| |||||||| ||||||||| | || ||||| |||| | | | |||| ||||| | | || |
-------------gtacggacgggagtctgtctctctctctctttcagtaatccctccc---attcatgcgcacaccatcctcgtatgcgtacgcacgagcgcattgcgtcagtaatgaacacgcacgcatgctctgctgtgcact---gcagGTGGACCTGACGGGCGGGTACTACGACGCGGGCGACAACGTGAAGTTCGGGTTCCCTATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
upper sequence: PP1S376_19V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
gtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggacctctgct-gaaat-tgtaaaattgaccttgacgat-ggtggactcttgtgcagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT
||| ||| || | | | | || | | | | || ||||| | | | || || || ||| | | ||| | | | ||| | | | | ||||| ||| ||| ||||||||||||||||| || |||||||| ||||||||| | || ||||| |||| | | | |||| ||||| | | || |
-------------------------gtacgtgcaccgacccagtccgactaataaatcac---tctctatagttgc---cttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgta-acagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
upper sequence: PP1S376_19V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G167669_T01 (Zea mays), 3'ss of exon 1
gtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggacctctgctgaaattgtaaaattgaccttgacgatggtggactcttgtgcagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT
| | ||| |||| | | | | | ||| | | | | | | || | | | || | | || || || | | | || |||| | |||| || || ||||||||||| ||||||||||| |||||||| | || ||||| ||||||||| || | || ||| | || || ||||
------------------------------------------------ggacctttttgacaatttttttcttttttctttttcaaaaagaaagaaggaagaattg--aagctcattgtgttcgtgtcgtcgttgctgctc-catatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGTTTCCCGATGGCGTTCAGCGTCACCCTCCTGAGCTGGAGCGCCGTCGAGT
upper sequence: PP1S376_19V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA08G04840.1 (Glycine max), 3'ss of exon 1
gtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggacctctgctgaaattgtaaaattgaccttgacgatggtggactcttgtgcagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT
| || || ||| | ||| |||| | | | || || | ||| | | | |||| || || || ||||| || ||||||||||||||||||||||| || || ||| | ||||||||| |||| ||||| |||| | ||| |||| ||| | | | | || |
-----------------------------------------------gtaagtttcttgttctgttatgaaaatgtagattgatagagaatatgat--gatgattaatgaggtaggcacattg----------tgttg----tttactcagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT
upper sequence: PP1S376_19V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA05G34850.1 (Glycine max), 3'ss of exon 1
gtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggacctctgctgaaattgtaaa-attgaccttgacg-atggtggactcttgtgcagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT
| | | | ||| | || | | | | |||| | | | ||| ||| || ||| | || | ||||| || ||||| ||||||||||||||||| || |||||| | ||||||||| |||| ||||| ||| | ||| |||| ||| | | | | || |
------------------------------------------------------------------gtaagtttttctgttttgt-tctgaaagggtaataggtagagaaaatgatgattaatgaggttggtacattgtgtttttttct-cagGTGGACTTGAGCGGAGGGTACTACGACGCCGGGGACAACATAAAGTTCGGGTTTCCGATGGCGTTCTCGACGACAATGCTGTCGTGGAGCGTGATCGATT
upper sequence: PP1S376_19V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA04G12290.1 (Glycine max), 3'ss of exon 1
gtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggacctctgctgaaattgtaaaattgaccttgacgatggtggactcttgtgcagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT
||||| | | | || | | ||| | | | | ||| || | | | || | | | ||| | | | ||| |||| ||||| ||||| |||||||||||||| ||||| |||||||| || || ||| |||||||||| | || | ||||| |||| |||| | | || |
---------------------------------agaaaagagaaggaataaatata----aaactaacaaactaacaacttttcgataaaaaagaaaatgcatcagtt-acattacatagccaaactttgt-atgg------------cagGTGGATTTAAGTGGAGGGTACTATGACGCAGGAGACAATGTGAAATTCAACTTTCCAATGGCCTACACCACTACCATGCTGTCATGGGCCACAATTGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggacctctgctgaaattgtaaaattgaccttgacgatggtggactcttgtgcagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT
ctcttgt CT-rich tract
tgaaattgtaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggacctctgctgaaattgtaaaattgaccttgacgatggtggactcttgtgcagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG