Sequence
atgc intronic sequence ATGC exonic sequenceTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcatcactttacgattctgctgttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccatttcggtactaggtt...
Basic information
species | Physcomitrella patens |
transcript | PP1S47_161V6.2 |
intron # | 16 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 5'ss of exon 16
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagc-atcactttacgattctgctgttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccattt--cggtactaggtt----------
||||||||||||||||||||||||||||| || ||||||||||| || || || || || | || || | | | | | | | ||||||| ||||| | | | || ||| || ||| || || || | || | | || || || | || | | | | || || | |
CATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAATTTGGAGAACATATTCGGTCAAGCTCCTGGTGTTGATTCGgtacaatctgataacctagctttcatttgctcaaaaccttttttccattataaccgatcttacgtttccatatgttgacatgctgactcgccgttatttgacaatctctccag
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: LOC_Os01g46750.1 (Oryza sativa), 5'ss of exon 16
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgag--catc-actttacgattctgctgttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccatttcggtactaggtt-----------------------------------------------------------------
|| |||||||| ||||| |||||||||||||| ||||||||||| || ||||| ||||| | || || | || | || || | ||| |||||| | ||| ||||| |||| | | ||| | |||| || || | ||| || | | | | | | | | || ||
CATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAATTTGGAGAACATTTATGGTCTTGTTTCTGCTATAGATTCGgtatatggctatctgctttaaagttctctgctccttaaatttattct-gcgacattgttt-ttgcctttttggtatcataaatgactgatgggtcattaccttctgtttctgctaaaacaatttgaaaaactttcctctgttttttttttttttgaacatctgttcag
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: LOC_Os06g06350.2 (Oryza sativa), 5'ss of exon 11
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcatcactttacgattctgctgttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccatttcggtactaggtt-
||||| | ||||| || || ||||||||||| || |||||||| |||||||| ||||| || || ||||||||| | | | ||| ||||| | ||| || | || | |||| | || | | || | | | || ||| | | |
CATTGACAGGAAGAAAAATATATTCAAGCTTTCACAGGGAGAATATGTTGCAGTAGAAAATCTCGAGAATGTGTACGGGGTTCTCCAAGAGATAGATTCGgtaactactatacta-actactcactttttcaggggatcgtctcaaattttatgtttctatctgatatgagcctttttttccctattatatttcccatatg
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: GRMZM2G152127_T01 (Zea mays), 5'ss of exon 16
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagc---atcactttacgattctgctgttca--taatctagttcttgcaaccacatgcactgctttagcagatttcga--tctacccatttcggtactaggtt
||||| ||||||||||||||||||||||| || || ||||| |||||||| || || || || || || | | | | | | |||||||| ||||| | || | | | | | || | | ||| | ||| | | | || || || | |||| | | | ||
CATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctcaaaacagtcttcatctacacagtctaagtgttctgcagcaaatggttacaaataattccataatccatctctaagtctaaacgatacatcttcag---
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: GRMZM5G812228_T01 (Zea mays), 5'ss of exon 11
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatg-agca---tcactttacgattctgctgttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccatttc---ggtactaggtt
|||||| | |||||||| || ||||||||||| || || |||||||||||||| ||||| || || |||||||| || | | ||| ||||||| | || ||||| | || | | || | | | ||| || ||| | |||| | |||||| ||| || |
GATTGATAGAAAGAAGAATATTTTCAAGCTTTCGCAGGGGGAATACGTTGCAGTGGAAAATCTAGAGAATGTGTATGGTGTTCTTCAAGATATAGATTCGgtatgtaacaaactcactggaaaatgc-acggtcttaactttttttccccatgttgcaacagaattttttata---ttcgtttcacccatgcttaaggtgcttg---
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 16
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagc-atcactttacgattctgctgttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccatttcggtactaggtt---
||||||||| |||||||| || || |||||||| ||||||||||| ||||| ||||||||||| || ||| | ||| | | || ||| |||| | ||||| | | | | | || || | | ||| ||| | | || | | | | ||| | | | ||| | || ||
TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctgactcctgagaatcctattccttccaat--ggttttggtgtcctaacttgtag--taaatttattaccaaaatcaaattggaaaaataagtagaa
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: GLYMA11G02030.1 (Glycine max), 5'ss of exon 16
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcatcactttacgattctgctgttcataatctagttcttgcaaccacatgcactgctttagcagatt--tcgatctacccatttcggtactaggtt
||||||||| |||||||| || || |||||||| ||||||||||| ||||| ||||||||||| || ||| | ||| | | || ||| |||| | ||||| | | | | | |||| | | ||| | | || || |||| || | || | | |||| | | ||
TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcc-tgagaatcctattccttccaatgtcccccagtattggtgcatgt-tgatctatattagtgatttagtgaatgtccacattctgtagttcagta
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: GLYMA05G36910.1 (Glycine max), 5'ss of exon 16
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTG-------ATGCGgtatgagcatcactttacgattctgctgttcataatctagttct---tgcaaccacatgcactgcttta--gcagatttcgatctacccatttcggtactaggtt----------------------------------------------------------------
||||||||| |||||||| || || |||||||| ||||||||||| ||||| || |||||||| || ||| | || | | | || ||||||| ||| | ||| | || | | || || || | | || | || | || | | || |||| ||| | | | | ||| || || ||
TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAACCTGGAGAATATTTATGTTCAAGCTTCTTCTGTTGAATCTgtatgtcttgtgaacccttctcttttaatcaacttatc-tgccttcattatgaatgatatcaaaaggtttggtttactgcaaagatagtaacaaaggttttagtttcagcttcatttcatgagcagataatgttccgtgatatgttgatattacttcttttccaactctatttcag
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: AT1G49430.1 (Arabidopsis thaliana), 5'ss of exon 16
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcatcactttacgattctgctgttcataatctagttcttgcaaccacatgcactgct--ttagcagat-ttcgatctacccatttcggtactaggtt
|| ||| | |||||||||||||||||| | |||||||| ||||| ||||| || |||||||| ||||| ||| | || ||| | |||||| || | ||| ||| || | | ||| | || | | | || || | || | || | | | | ||||||| || || ||
CATCGATAGGAAGAAGAACATCTTCAAGTTGTCTCAAGGTGAATATGTTGCTGTTGAAAACCTCGAAAACACTTACTCAAGATGTCCCCTCATTGCTCAGgtatgta-atta--ttaaaattatgttttcaatactataatcatagtaattgaata-attgttatctaataattgtactatctaccaataattgtgacag---
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: AT1G64400.1 (Arabidopsis thaliana), 5'ss of exon 14
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcatcactttacgattct--gctgttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccatttcggtactaggtt
|| || || |||||||||||||| || || |||||||||||||||||||| || || ||| | || || | |||| | | | || | |||| |||||| || | | || | ||| | | | | || ||| | | | ||| ||| | | || || |
CATCGACCGTAAGAAGAACATCTTTAAACTGTCTCAAGGAGAATACGTTGCCGTTGAGAACTTGGAGAACATATACAGTCATGTCGCCGCCATTGAATCGgtattagt-tgaaaatataactcttaagtaaccgttacataaaactt--agcta-atgatctgttaaaacattttgcag-----------------------
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 16
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatga---------gcatcactttacgattctgctg--ttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccatttcggtactaggtt
||| || |||||||||||||| ||||||||||| ||||||||||||||||| || || ||| | ||||| | || | || | |||| ||||||| | ||| |||| || ||| || || | || || | | | | || | ||| |||| | | ||
TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtgtcatcatacgttttacctgaatttatcactcctttttttcccctgattttggttctctctcag-tttcattgtgtatgcctct----------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|6102274|gb|AW126744.1|AW126744EST: AGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGAATGCG TCCCAAATCAACAAGCATTA
genomic: AGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGA-TGCGgtatgagcat ... gctgtagcagTCCCAAATCAACAAGCATTA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcatcactttacgattctgctgttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccatttcggtactaggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC