Sequence
atgc intronic sequence ATGC exonic sequencegtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
Basic information
species | Physcomitrella patens |
transcript | PP1S81_165V6.4 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 12
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
| | | |||||| | | || | || ||| ||| || ||| | || || | ||| | || ||| ||||||||| || |||||||| |||||| ||||||||||||| || ||||| || |||||||| |||| || || || || || ||||| || ||||| || ||
----------------------------gtaactatgtttgcttcacacaggataaggttgt-tacacatcttattact---ggtctctattgtactaagttgtgaagttccctattattatt-tgcagATCCTACCTACATGATCCGAGCTATTCCAAGCAATGCATCAGACAATGTCTACTGCACGCTGCTGGCCCACAGTGCTATTCATGGTGCAATGGCCGGCTA
upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
---gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
| | | | | | || | | |||| | || || || || | | ||| | | | | | | | | ||| | || | | | | ||||||||||| |||||||| || || ||||||||||||| || ||||| || |||||||| |||| || || || ||||| ||||| || ||||| || ||
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgca-ataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
| || || | ||| | ||| | | | || |||| | || || | || | | |||||||||||||||||||||| || || | ||||||||||||||||| ||||| || ||||| |||| ||||| |||| |||||||||| ||||| || ||
-------------------------------------gtcagtggttttcttcggtg-tcatatttcagggccagaactgctagttacacacat-ctcagatgt-----ttcttc------tactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 12
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
| | |||||| | |||||| || | || || | | || ||| | | | || ||| | ||| | || || ||||||||| |||||||| || ||| ||||||||||||| || ||||| || || ||||| |||| || ||||| ||||| ||||| || ||||| || ||
-------------------------gtaatcgtcttcttttttacttggtgaacgcagtgtta-gtttgtaa-----tttatagcatgtcaaggaatctgatg-aagtgcctgccatttttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTATTGCACCCTGCTCGCACATAGTGCCATTCATGGTGCAATGGCGGGATA
upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 11
gtggccat-atgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
| | | | | | | | | | || | | | | | || ||| || | || | ||| ||| || | | | | | || | | | | | ||| ||||||||||||| ||||| ||||||||||||||||||||||||||||||||||||||||| | |||||||| || || | |||||||| |||||||| ||
--gttcgttaagacaaactatacaattatacgtatgtgtgca-tgtttgatt---atatttatgtatgcattgcatactgaaaggaggaaatcaagcatt-------gcattttttttactatttgacagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA
upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 11
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaa-attc-cttttagtcgtttttaggcttgaatatgagtactcaccacatg-attctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
| | | | || || || |||| || | | | | | | | |||| || | | | | | | || | |||||||||| || |||||||||||| |||||||||||||||||||||||||||||||||| | |||||||| || || | |||||||| |||||||| ||
----------------------------------gtttgtaaagattaaacttcatggaattataagtgtgcacacacacactgaaaagagcaatggctgaaagagtaatgccttctctttatgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 11
gtggccatatgcccagttgaaaacttttggttttttc-tttgc-tgcttg-gttctcgtgcttctatattcatgaaattccttttagtcgtttttagg--cttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
| | || || |||||| | ||| | | | || | | || || | || | || ||| ||| | | ||| | | || | | ||| ||||||||||||| ||||| ||||| ||||||||||||||||||||||||||||||||||| | |||||||| || || | |||||||| |||||||| ||
--gttcgtaaagacaa---aaaactatatatttatacgtatgtgtacatgtgtgcatgttcgattacatttatgtgtgcattgcatactgaaaggaggaaatcaagcattgcatttttttttactatttgacagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA
upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtac--tcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
|| | | || || ||| | | | || || | | |||| || | | | | || | || | |||||||||| || ||||| |||||| ||||||||||||| |||||||||||||||||||| | |||||||| || || | |||||||| |||||||| ||
---------------------------------gtttgtaaagattaaaagttcatggaattatgtgtgtacacacactgaaaggagcaat--ggctgaaagagtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA10G33820.1 (Glycine max), 3'ss of exon 12
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
| | || || | | | ||||| |||||| | || ||| || ||||| || | ||| | | | || ||||||||| ||||||||||| ||| ||||||| ||||| || |||||| | ||||||||| | ||||| ||| | || | |||||||||||||| || ||
--------------------------taaaatcaactaatgatgggggcagttgttacttctctattca-aatcttgaattttgttgtttt--atttttattataaaacttgtttgtttactttcatagATCCAACATACATGATTCGGGCTATTCCAAGTAATGCCTCGGACAACATTTACTGCACTCTTCTTGCACATGGTGCTGTTCATGGAGCTATGGCTGGATA
upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 10
--------------------------gtggccatatgcccagttgaaaactt--ttggttttttctttgctgcttggttctc----gtgcttctatattca--tga-----aattccttttagtcg--tttttaggct---tgaatatgagtac-tcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
| | | || || || | ||| || || ||| ||| | || | | || || | ||| ||| | || ||||| | | || | | || | ||| || | | | || |||||||||| ||||||||||| || ||||||||||||| || ||||| || ||||| || | |||||||| || || ||||||| || |||||||||||
gtcagtttctcttacagcattctcctcttcctttttgacctatttatttcttacttagtctttcatttttatttcggatttgaaaggttttttaaaatttgactgacaattatctcattttaattgagttatctgcctagtgggataagactttgttgttattgtatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 11
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgct-tctatattcatgaaattccttttagtcgtttttagg---cttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
|| | | ||||| | | ||| | || || | | ||||| | | | | | | | | |||||||||| |||||||||||||||||||| |||||||| || ||||| || || || || | || ||||| || || | || || || ||||| || ||
------------------------------------------------------gtacaatttatatcccttgcattgcattctctccaccatgagtttcttgattgttcatttttcttgtcttaattt-cagATCCAACATACATGATTCGAGCTGTTCCTAGCAATGCGTCAGACAATGTTTATTGTACACTTCTGGCTCAGAGTGCAGTGCACGGTGCAATGGCTGGATA
upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT4G29220.1 (Arabidopsis thaliana), 3'ss of exon 11
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
| | | || | ||| || ||||||||| || || | | || || || || ||| | || ||||| | | | |||||||||| |||||||| ||||||||||| |||||||| || ||||| || | |||||| | | ||||| ||||| | ||||||| ||||| || ||
----------gtata-tagatatcttatgagtttttcttttgtgtatgtggaacata-------atagataaagtttcttct--tcttttttggt-------------------------gtctttcagATCCAACCTACATGATACGAGCTGTTCCGAGCAATGCATCAGACAATGTATGCTGCACGCTTTTAGCTCAAAGCGCGGTTCATGGAGTGATGGCTGGTTA
upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 11
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattcct-tttagtcgtttttaggcttgaat-atgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
|| | | | | || |||||| | || | | | ||||| | | || || | || | ||||||| || |||||||| |||||| ||||| |||||| ||||||||||| |||| ||| | ||||| || ||||| ||||||| || ||||| || ||
------------------------------------------------------gtacgtttgtcctccccaaattcaagtcgagctacatagattcatgaattagaaatatgactcaaaccatgtttcagATCCGACATACATGATCCGAGCTATTCCAGCCAATGCATCTGACAACGTCTACTCAACTCTCCTTGCCCAAAGCGCAGTCCATGGTGCAATGGCTGGCTA
upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 11
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgc-ttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
||| | | | | | | | | || | | | | || | | | ||| || | | | ||||||| ||||| ||||| || ||||||||||||||||| |||||||| || || ||||| | |||||||| || || | |||||||| |||||||||||
------------------------------------------------gtttgtatacactatctttctaatatatagaagctgggcaatggctggtctaacca--agtgctgcactttttgtctatcagATCCTACGTATATGATCCGTGCTGTTCCAAGCAATGCATCTGACAATGTCTATTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGGTA
upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 11
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
|| |||| | ||| | || | || || || ||| || ||| || | | | | || || ||| | ||||| || ||||||||| || |||||||| || ||| ||||| ||||||| |||||||| ||||||||||| | |||||||| || || | |||||||| |||||||| ||
---------------gtcagtgacttcagatttgtgtttgtttatttatttttc---cttttagatttg---gcttagtaacaatagattctaagct--atcctgagttgtc-----------ttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA
upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv16s0013g01140.t01 (Vitis vinifera), 3'ss of exon 12
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcacca-catgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
| |||| | ||| | ||| | || | | | || || ||| | || ||| |||| || | | | | || ||| |||||||||| |||||||| |||||| ||||||| ||||| || ||||| | |||||||| | ||||| ||||| || | ||||| || |||||||||||
----------------------------gtttttattgttgata-ttgctaactgt-ttattcttttaataggattttatctaaaaaaatttcaaagattatatttttatttattatcttgtctctacagATCCAACATACATGATCCGAGCTATTCCAAGTAATGCATCAGACAATATCTACTGCACCCTCCTTGCACATAGTGCTGTACATGGGGCCATGGCAGGGTAMapped 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|162256335|gb|FC432345.1|FC432345EST: GAATTTAAGGAGCCGCTGAACTTGAAATACATAG ATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGT
genomic: GAATTTAAGGAGCCGCTGAACTTGAAATACATAGgtggccatat ... gattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
tactcac putative branch site (score: 1)
ttgaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT