Sequence
atgc intronic sequence ATGC exonic sequence...tatcctaagtcgagtgtaaaacattgagttaagtaaggtgtattcctttcttgtgatataaaggctgacccatttggtgttctctgactgttctgtatagGTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTG
Basic information
species | Physcomitrella patens |
transcript | PP1S307_14V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S307_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
--tatcctaagtcgagtgtaaaacattgagttaagtaaggtgtattcctttcttgtgatataaaggctgacccatttggtgttctctgactgttctgtatagGTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTG
| | || | | | | || | | || ||| || | || | | || || | | ||| | | |||||||| |||||||||||||||||||| || |||||| | ||||| |||||||| ||||| |||||
ggaggggtttttttggtttcaggcccgagg--gggttccttttttttttttttttggggggggggggggggcgggggggcttttttggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
upper sequence: PP1S307_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
-----tatcctaagtcgagtgtaaaacattgagttaagtaaggtgtattcctttcttgtgatataaaggctgacccatttggtgttctctgactgttctgtatagGTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTG
||| || | | | ||| ||| | || | |||| | | | ||| | ||| ||| | || |||| || | ||||||| |||||||||||||||||||| || |||||| | ||||| |||||||| ||||| |||||
gaggttattgattgtggggatggggattttgggttttggaactgatggggcttttctttttttcttttcttgaactttttt-tgtggtttg--tgttttgaa--gGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
upper sequence: PP1S307_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA04G01140.1 (Glycine max), 3'ss of exon 2
tatcctaagtcgagtgtaaaacattgagttaagtaaggtgtattcctttcttgtgatataaaggctgacccatttggtgtt-----ctctgactgttctgtatagGTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTG
|| | | ||| | || || || | | | | | | | || || | ||||| | || ||| | | | ||| | |||||||||||||||||||||||||| || || ||||| | ||||| ||||||||| |||| || ||
-----aaaatggtaagtagtagcttttttttagaatcgagaagctgtgggatcttatctagattctgacttgtgtgatgtaagttgtttaaaattttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG
upper sequence: PP1S307_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA06G01180.2 (Glycine max), 3'ss of exon 1
tatcctaagtcgagtgtaaaacattgagttaagtaaggtgtattcctttcttgtgatataaaggctgacccatttggtgtt-----ctctgactgttctgtatagGTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTG
|| | | ||| | || | || | | | | | | | || || | ||||| | | || ||| | | | ||| | |||||||||||||||||||||||||| || || ||||| | ||||| ||||| ||| |||| || ||
-----aaaatggtaagtagcagctttttgttagaatcgagaagctttgggatcttatgtagattctgactcgtgtgatgtaagttgtttaaaattttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTG
upper sequence: PP1S307_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT4G39100.1 (Arabidopsis thaliana), 3'ss of exon 2
tatcctaagtcgagtgtaaaacattgagttaagtaaggtgtattcctttcttgtgatataaaggctgacccatttggtgttctctgactgttc---tgtatagGTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTG
| ||| || | ||| | | || || | | ||| ||| | ||| | | | ||| || | ||| | || | | |||| || || ||||||||||| ||||| |||||||| |||||||| ||||| ||| || || ||
gttaataattcattgatttgtcatctaaattggtttcatgaagttgttt-ttgcaaagagaag--taatcaattgagtttaaattgattttttctgtttgcagGTTCTGCAAGTGTGAGATGCCGTATAACCCAGATGACTTGATGGTGCAATGCGAGGAGTGTTCTGAGTG
upper sequence: PP1S307_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
tatcctaagtcgagtgtaaaacattgagttaagt-aaggtgtattcctttcttgtgatataaaggctgacccatttggtgttctctgactgttctgtatagGTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTG
|||| | | || | | | | | | | || ||| | | || | | | | | | | | | |||||||| ||||| |||||||||||||| ||||||||| | ||||| || || ||| ||||| || ||
---------gtgagtttgagttgttttgctggattgatgattgatgattgaatgtactggtattcgtgggctgatgaatacttttgaattttgtattgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG
upper sequence: PP1S307_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ16306 (Selaginella moellendorffii), 3'ss of exon 2
tatcctaagtcgagtgtaaaacattgagttaagtaaggtgtattcctttc-ttgtgatataaaggctgacccatttggtgttctctgac---------tgttctgtatagGTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTG
||| || | || | | | || | || ||||||| || || | | | ||| ||| || | || || |||||||| |||||||||||||| || ||||| || |||||||||||||| || ||| | ||||| |||||
--------gtct--cgttgtgttcgaacttctctttcctctcttggtctcgttgtgatcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG
upper sequence: PP1S307_14V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ17782 (Selaginella moellendorffii), 3'ss of exon 2
------------------------------------------------------------------tatcctaagtcgagtgtaaaacattgagttaa-gtaaggtgtattcctttcttgtgatataaaggctgacc---catttggtgttctctgac---------tgttctgtatagGTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTG
| || | || || | ||| ||| | | | | |||| || | | || | | | | ||| ||| || | || || |||||||| || ||||||||||| || ||||| || |||||||||||||| || ||| | ||||| |||||
gtaagtgctctctctctccctctgtctctctggcgtctcgttgactagttgtgttcttatcaagcttctctttcttctcttg-gtctcgttgtgttcttatcgaacttctcctgttctcgttgtgttcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTGMapped 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|162178126|gb|FC354428.1|FC354428EST: TTTGAATACAAGGCTTCTACTGGCGGATTCACTCCTGATCGAGTGGCTGT GTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATG
genomic: TTTGAATACAAGGCTTCTACTGGCGGATTCACTCCTGATCGAGTGGCTGTgtacgtcatt ... ttctgtatagGTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttcttgtgatataaaggctgacccatttggtgttctctgactgttctgtatagGTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTG
ctctgac putative branch site (score: 3)
ctgttct CT-rich tract
tgatataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatcctaagtcgagtgtaaaacattgagttaagtaaggtgtattcctttcttgtgatataaaggctgacccatttggtgttctctgactgttctgtatagGTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG