Sequence
atgc intronic sequence ATGC exonic sequenceGGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatagcgtacatctcactcaacatcaggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgatatatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
Basic information
species | Physcomitrella patens |
transcript | PP1S117_16V6.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os01g66120.1 (Oryza sativa), 5'ss of exon 2
---------GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatagcgtacatctcactcaacatcaggagtaaacctgtcgatcatgcta-gttgcctatgattcctgaatcgatatatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
||| |||||||||||||| ||||||||||||||||||||||| ||||| || || |||| || || | | || | | || | ||||| | | | ||| | | ||||| |||| | | | || ||| ||||| ||| | || || || ||| | || |
CGCCGGCAAGGCGCCCAAGGGCGAGAAGACCAACTGGATCATGCACGAGTACCGCCTCGCCGA-----CGTCGACCGCTCCGC-CCGCAAGAAGAACAGCCTCA---GGgtaagcaaaaaccacacccaagattccatcac---taaattcattactaaatctgtgttcatcgtgattattga-ttaattta-gtcacctaattattcgcccaa---------------------------
upper sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os05g34830.3 (Oryza sativa), 5'ss of exon 1
---------GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatagcgtacatctcactcaacatcaggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgatatatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
||| ||||||||||| || ||||||||||||||||||||||| ||||| || || |||| || || | | | | | || | |||||| |||| | | | | | | | || | | | |||| | | || | | | || ||| | | | | || | || |||
CGCCGGCAAGGCGCCCAAGGGCGACAAGACCAACTGGATCATGCACGAGTACCGCCTCGCCGA-----CGTCGACCGCTCCGC----CCGCAAGAAGAACACCCTCCGGgtacatata-tacgccattaattaattacctcgaatttgctcttaattcat-caaatt-----caaattcaga--cgaattctactctcagttaatcaagtttagacaa----------------------
upper sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os11g08210.1 (Oryza sativa), 5'ss of exon 2
GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCG-Ggtatgtatagcgtacatctcactcaacatcaggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgatatatgttgcctgtggaccagcgaatg-acgcccgtctaattttgtggctgcag
|| || ||||||||||||||||||||||| ||||| || || | | || | || || | | | | |||| | || || | | | | || | || | ||| | || | | |||| || | ||| |||| ||||| || ||| | | |||||
------------CGTCAAGACCAACTGGATCATGCACGAGTACCGCCTCGCCGACGTCGACCGCTCCGCCGCCGCCCGCAAGCTCTCCAAGTCCTCCCACAACGCCCTCAGGgttagtatttacttcttttaattacttacttctc--ctaatctaatcatctcttgctttc-aatc-----atttctcctc---accaacgaatttacccccattttatttt----------
upper sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os12g03040.1 (Oryza sativa), 5'ss of exon 2
GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatagcgtacatctcactcaacatcaggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgatata-tgttgcctgtggaccagcgaatgacgcc-cgtctaattttgtggctgcag
|| ||| ||||||||||||||||||||||||| | ||| || | || || |||| || | | ||| ||| | |||| | | ||| ||| | | | | || || | ||| | | | | | | | || || | | | || |||| |||| |||
---------------CAAGACCGACTGGATCATGCACGAGTATCGCCTCAC---AGGCACATCAGCTAA----CAACACCACCACCACAA--------AGCAGCGTAGAGCAT-CATCCA--TGACCATGAGGgtgagattcatttaattacttaattttagttcattattaatttgtttttctcttcgtcgtacgtcttctttgaaagctacgtcgttgtttgaattggcat
upper sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os03g21060.1 (Oryza sativa), 5'ss of exon 2
GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatagcgtacatctcactcaacat-caggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgatatatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
|| ||||||||||||||||||||||| ||||| || | | | ||||| | | ||| |||| | || || || | | | | | | ||| | | || | | | | | | || || || | | || || || || | | | | || | || || || | | || ||| |
---------------CAAGACCAACTGGATCATGCACGAGTACCGCCTCGCCGCCGCAGA--CGCCCACG--CCGCCAACACC--TACCGCCCCATGAAGTTCCGCAACACCTCCATGAGGgtaagcaagctccatctacgttacctagca-gccagattcaaattat--ctaaaccaa-acaacttaattatgaac----aaaccctagcagctggatcttgctatcg---
upper sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G014653_T02 (Zea mays), 5'ss of exon 1
---------GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtata-gcgtacatctcactcaacatcaggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgata-tatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
||| |||||||||||||| ||||||||||||||||||||||| ||||| || || || | | |||| | | | | | | ||||| | | | ||| | | | | || | | | | | | | | | | ||||| | ||| || | | |
CGCCGGCAAGGCGCCCAAGGGCGAGAAGACCAACTGGATCATGCACGAGTACCGCCTCGCCGA--------CGTCGACCGCTCGGCG-CGCAAGAAGAACAGCCTCAGGgtaagaacaagcgctccgccgccgtccgtccgtccgttggcgtcgtcaccgtccaaatcaaacaaaaagaacttggcgataatgtgtcgctttcgtaatg---------------------------------
upper sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G123667_T03 (Zea mays), 5'ss of exon 2
GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAG--GGGTG-TCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatagcgtacatctcactcaacatcaggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgatatatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
|||||||||| || ||||||||||||||||||||||| ||||| || || | | | ||| || | || | | | | | | | | | ||||| || |||| | | ||||||| ||| | | ||| | || | | | || | | || || ||
---GCCCAAGGGCGTCAAGACCAACTGGATCATGCACGAGTACCGCCTCGCGGACGTCGACCGCTCGGCCGCCGCACGCAAGAAGACCAACAACGCGCTCAGGgta---attcactacaccatgacctttctcaggag--aacatatttatctccccgaaatactgacacttgcagttagagggaaaaaatatagagagaagtaaaaa--------------------------
upper sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G180328_T01 (Zea mays), 5'ss of exon 2
------GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGG----GTGTCGCCCTCT-GCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatagcgtacatctcactcaacatcaggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgatatatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
||| ||||||||||| || ||||||||||||||||| ||||| ||||| || || | | ||||| | | | || || | | || | ||||| | || | | | | | | | || || | ||| | || | | || || || ||| ||||| || | |
CGGCAAGGCGCCCAAGGGCGACAAGACCAACTGGATCATGCATGAGTACCGCCTCGCCGACGTCGACCGCACCGCCCGCAAGAAGAACAACAGCCTCAGGgtacgttgcgatcg-atcgagt-tccggccggcgcgtccaccagaatatctcattcgtttctgt--gcagaaaattatctcttgctcg-tatatattattatttg-------------------------------------
upper sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G011598_T01 (Zea mays), 5'ss of exon 2
GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatagcgtacatctcactcaacatcaggagtaaacctgtcgatcatgctagttgc-ctatgattcctgaatcgatatatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
| || ||||||||||||||||||||||| ||||| || | | | | | | || ||| |||||| || || | | | | || | ||| | || || || || |||| | || | || ||| | ||| | | | | | | ||| | | | ||
------------CACCAAGACCAACTGGATCATGCACGAGTACCGCCTCGCCGCCGACGCGCAGGCA---GCGCACGCCTACCGCC------CCATGAAGTTCCGCAACGCCTCCATGAGGgt--acgtcgtacgttg-ttaatcactcatctgatttaaaccataccccctcttgccataca-ataatccaagaaaaaccgagttagattcaaagaacaaaaat-------
upper sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA14G24220.1 (Glycine max), 5'ss of exon 2
---------GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatagcgtacatctcactcaacatcaggagtaaacctgtcgat-catgctagttgcctatgattcctgaatcgatatatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
|| |||||||| |||||||| ||||||||||||||||||||||| ||||| || | || ||| || | || | | | | || || |||||| | | | | |||| |||| | | | | | | | | | || | | || | |||| | | | | | | ||| |||
CGCTGGAAAAGCGCCCAAGGGAGAGAAAACTAACTGGATCATGCACGAGTATCGTCTTGCAGACGTGG-ATCGT--TCCGTTCGCAAAAAGAACAGC------TTAAGGgtatattcccctttc-tctc-ttcaatacgaaggacataatggacatttcgtggcacaaatattacctttcgaaatcaccgttt--tactttt--acccttaaata--------------------------
upper sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA13G35550.1 (Glycine max), 5'ss of exon 2
------------------GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatagc-gtacatctcactcaacatcaggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgatatatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
|||||||||||| |||||||| ||||||||||||||||||||||| || | | || | ||| |||| | | | || | | | | | | | | || |||| || || | || ||| ||| | |
CGTTTTCTACGTTGGCAAAGCCCCCAAGGGCACCAAAACCAATTGGATCATGCACGAGTATCGCCTCCTCGAC----TCTTCCCGAAAGAACACTGGCACCAAGgtatacagctacacatacacacatccacatactctgtttcttaattgttttacacct-tcaattaattagaatgtcta--attgcag-----------------------------------------------------------
upper sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA12G22880.1 (Glycine max), 5'ss of exon 2
------------GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgta-tagcgtacatctcactcaacatcaggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgatatatgttgcc-tgtggaccagcgaatgacgcccgtctaattttgtggctgcag
|| ||||| ||| |||||||| |||||||||||||||||||||||| || |||| | | | | ||| || ||| || |||| || | | | | || | | | | || || | |||| | || | |||||| | || || | | || || |||
CTACGTTGGCAAAGCACCCAAAGGCTCCAAAACCAATTGGATCATGCACGAGTATCGCCTTCTCGA------------CTCTTCCCGCAAACACAACCTCGGAACCGCAAAGgtacataattacattcccttccccctgtttt-----tcaagctcttactcat---aatttcttatgatactaaggattatgaatttcatcgtggtgattttaaaatcg-------------------------
upper sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA06G38410.1 (Glycine max), 5'ss of exon 2
------------GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatagcgtacatctcactcaacatcaggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgatatatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
|| ||||| ||| |||||||| |||||||||||||||||||||||| || ||| | | | | ||| || ||| || |||| | | ||||| | | || ||||| ||| ||| | | || ||| || | |||| | | | || | || | | |||
CTACATTGGCAAAGCACCCAAAGGCTCCAAAACCAATTGGATCATGCACGAGTATCGCCTTCTCGA------------TTCTTCCCGCAAACACAACCTCGGAACCGCAAAGgtacacacaat-tacattct--ctagcttcc--------cctgtttttcaagctc-tcactcataatttctta--tgatac-taaggattctgaatt--tgatcattgttattttaa--------------
upper sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA02G26480.1 (Glycine max), 5'ss of exon 2
---------GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatagcgtacatctcactcaacatcaggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgatatatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
|| |||||||| | |||||| ||||||||||||||||||||||| || || || | || ||| | | | || | | | | | | | | | | ||| ||| | | | | | || || ||| |||| | | | || | |
CGCCGGAAAAGCGCCCAAGGGAGTGAAAACTAACTGGATCATGCACGAGTATCGTCTCGCCGACGTGG-ATCGTTCGGTTCGCAAAAAGAACAGCTTAAGGgtatataccagtatgcgcccttttttctcttcactatcgaggacataatagac-atttcaacgcacatttacctttcgaaaatcaccgttt--taccctttaa------------------------------------
upper sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA12G35000.1 (Glycine max), 5'ss of exon 2
------------------GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatagcgtacatctcactcaacatcaggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgatatatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
|||||||| ||| |||||||| ||||||||||||||||||||||| || | || | | | ||||| | | | | || || ||||| | | || | ||| || | | ||| | | | | || | | || | || |
CGTTTTCTACATTGGCAAAGCCCCCAAAGGCACCAAAACCAATTGGATCATGCACGAGTATCGCCTCCTCGA----------CTCTTCCCGAAAAAACACCGGCACCAAGgtatatacacagctacag--tacattttttctatcaataaaagttaatttttttatcttttttagtattattagtttttattaacggagatttaaactttca-------------------------------------
upper sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA06G16440.1 (Glycine max), 5'ss of exon 2
---GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCC--TCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgt---atagcgtacatctcactcaacatc-----aggagtaaacctgtcgatcatgctagttgcctatgattcctg-aatcgatata-tgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
|||||||| || | ||||||||| |||||||||||||| |||||||| || | ||| | || ||||| | | | | | | |||| |||||||| | | ||| || ||||| | | | | ||| | | || || ||| || ||| || |||| | | |||| || |
AAAAGCCCCCAAAGGAGTGAAAACCAATTGGATCATGCACGAATATCGCCTCGCCAA-----TGTTGACCGATCTGCCTCCAAGAAAAACAACAACAACTTGAGGgtatgtcccaaattgta-atttcactagtttttcttttatgggcaaa--tattaattttgttagaatgttagttttcttgcaatcttttttctgtttccctta--------------------------------------
upper sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
------GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatagcgtacatctcactcaacatcaggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgatatatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
|| || ||||| ||||||||||| ||||||||||||||||| || || || || | | | || | || | | | | | ||||||| | | |||| | ||| | | || || | | || ||| | | | | |||||| | ||||| | | | ||||
CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGGTCC---GTTCGCAAGAAGAAGAATAGTCTCA---GGgtatggaat---cagatctgattcacatctttgtttcaatctcttgttct-----gtttctggtaaat--tgaatcaacg-gtgttgatttttgcccag--------------------------------
upper sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv07s0031g02610.t01 (Vitis vinifera), 5'ss of exon 2
---------GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCC-GCGGCTCC--TTGCGGgtatgtatagcgt---acat-ctcactcaacatcaggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgatatatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
|| |||| || | |||||||| ||||||||||||||||||||||| || | | | || | | | | || | || | | ||| | | || | | | || | | | | || | ||| | || | ||| | | || ||||||| || || ||
TGCCGGCAAAGCTCCCAGAGGTGTCAAAACCAATTGGATCATGCACGAGTATCGCCTCGCCAATGTTGATCGATCCGCCGGCAAGAAAAACAACTTAAGGgtacgattgtaattctatactacattaaagatatttatttattatttaaaaaaaaaagaaaaagagtgatggttcttttt---------attgatatatattattattgactttgcag-----------------------------Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|162155197|gb|FC331173.1|FC331173EST: CTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGG CTGGACGATTGGGTGTTGTGCCGCATTTACGAGAAATGCACGCACGCGCAA
genomic: CTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatag ... gtggctgcagCTGGACGATTGGGTGTTGTGCCGCATTTACGAGAAATGCACGCACGCGCAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatagcgtacatctcactcaacatcaggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgatatatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG