Sequence
atgc intronic sequence ATGC exonic sequencegtgcagtcattattttcgtagaatacattgctttatttatctgcttatatggaagtcattttctttggcattctcaacctgtgagactgcggtatggtgttgttggacgcgttgctgtaacaaccgtgtttacactgactaacttcgacatcacatccttcgtattttagGGACTGTTGTGGACTCGAAGATTTGTCACCCTACGGAGTTTGACTTTTATCTTTGCAGTCATGCTGGAATTCAG
Basic information
species | Physcomitrella patens |
transcript | PP1S7_194V6.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GRMZM2G045821_T01 (Zea mays), 3'ss of exon 10
gtgcagtcattattttcgtagaatacattgctttatttatctgcttatatggaagtcattttctttggcattctcaacctgtgagactgcggtatggtgttgttggacgcgttgctgtaacaaccgtgtt-tacactgactaacttcgacatcacatccttcgt---attttagGGACTGTTGTGGACTCGAAGATTTGTCACCCTACGGAGTTTGACTTTTATCTTTGCAGTCATGCTGGAATTCAG
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--------------------------------------------------------------------------------gttagttctcgat---gtgtccttcattgcattt---taagatttattttataatctgaatgtcctaaaactctttttttgtgtggaaatatagGCACTGTGGTGGACTCGAAGATCTGCCATCCAACTGAGTTTGATTTCTACCTGTGCAGCCATGCTGGCATTCAG
upper sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 18
gtgcagtcattattttcgtagaatacattgctttatttatctgcttatatggaagtcattttctttggcattctcaacctgtgagactgcggtatggtgttgttggacgcgttgctgtaacaaccgtgtttacactgactaacttcgacatcacatccttcgtattttagGGACTGTTGTGGACTCGAAGATTTGTCACCCTACGGAGTTTGACTTTTATCTTTGCAGTCATGCTGGAATTCAG
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----------------------------------------------------------------ttaataacattactctat----ttggaatactctccaattgcatctgccagcaatgtaat--tattagtcccagagagttgaaacatctgtgattggttaatgtagGTACTGTGGTGGATTCTAAGATCTGTCATCCTACGGAATTCGACTTCTATTTATGCAGTCATGCGGGAATTCAG
upper sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 18
gtgcagtcattattttcgtagaatacattgctttatttatctgcttatatggaagtcattttctttggcattctcaacctgtgagactgcggtatggtgttgttggacgcgttgctgtaacaaccgtgtttacactgactaacttcgacatcacatccttcgtattttagGGACTGTTGTGGACTCGAAGATTTGTCACCCTACGGAGTTTGACTTTTATCTTTGCAGTCATGCTGGAATTCAG
| ||||| | |||||| ||||| ||| | ||| | || | || | | || | |||| | || | | || | || | | || ||| |||| |||| ||||| || || |||||||| || || || | ||||||||||||||||| ||||||||||| ||||| |||
-----------------------------gtaatattttcttacttata--------attttatttag-attat--gtcttgatggttgagct-tgat-ccgttgatcaaacaatctccact-ctagaatagcaat-acggttgttacaagcatgaagttcctattgtagGTACTGTGGTCGATTCGAAGATCTGCCATCCCAGTGAGTTTGACTTTTATCTATGCAGTCATGCAGGAATCCAG
upper sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: EFJ19862 (Selaginella moellendorffii), 3'ss of exon 17
gtgcagtcattattttcgtagaatacattgctttatttatctgcttatatggaagtcattttctttggcattctcaacctgtgagactgcggtatggtgttgttggacgcgttgctgtaacaaccgtgtttacactgactaacttcgacatcacatccttcgtattttagGGACTGTTGTGGACTCGAAGATTTGTCACCCTACGGAGTTTGACTTTTATCTTTGCAGTCATGCTGGAATTCAG
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------------------------------------------------------------------------------------------------gtgctgttgc---cgtt--tataagtggcgaatttaga-taactaa-tgagagaccgttttcct----tcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG
upper sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 17
gtgcagtcattattttcgtagaatacattgctttatttatctgcttatatggaagtcattttctttggcattctcaacctgtgagactgcggtatggtgttgttggacgcgttgctgtaacaaccgtgtttacactgactaacttcgacatcacatccttcgtattttagGGACTGTTGTGGACTCGAAGATTTGTCACCCTACGGAGTTTGACTTTTATCTTTGCAGTCATGCTGGAATTCAG
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------------------------------------------------------------------------------------------------gtgctgttgc---cgtca--ataagtggcgaatttaga-taactaa-tgagagaccgttttcct----tcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG
upper sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: EFJ19863 (Selaginella moellendorffii), 3'ss of exon 17
gtgcagtcattattttcgtagaatacattgctttatttatctgcttatatggaagtcattttctttggcattctcaacctgtgagactgcggtatggtgttgttggacgcgttgctgtaacaaccgtgtttacactgactaacttcgacatcacatccttcgtattttagGGACTGTTGTGGACTCGAAGATTTGTCACCCTACGGAGTTTGACTTTTATCTTTGCAGTCATGCTGGAATTCAG
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------------------------------------------------------------------------------------------------gtgctgttgc---cgtta--ataagtggcgaatttaga-taactaa-tgagagaccgttttccttga----cagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGGCGGCATTCAG
upper sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: EFJ14096 (Selaginella moellendorffii), 3'ss of exon 17
gtgcagtcattattttcgtagaatacattgctttatttatctgcttatatggaagtcattttctttggcattctcaacctgtgagactgcggtatggtgttgttggacgcgttgctgtaacaaccgtgtttacactgactaacttcgacatcacatccttcgtattttagGGACTGTTGTGGACTCGAAGATTTGTCACCCTACGGAGTTTGACTTTTATCTTTGCAGTCATGCTGGAATTCAG
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------------------------------------------------------------------------------------------------gtgctgttgc---cgtta--ataagtggcgaatttaga-taactaa-tgagagaccgttttcct----tcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGMapped 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|162213696|gb|FC390311.1|FC390311EST: CAATCACAATGATAATCGCTCTACGGATAGAAGTGGCAACATTTTACCAG GGACTGTTGTGGACTCGAAGATTTGTCACCCTACGGAGTTTGACTTTTATC
genomic: CAATCACAATGATAATCGCTCTACGGATAGAAGTGGCAACATTTTACCAGgtgcagtcat ... cgtattttagGGACTGTTGTGGACTCGAAGATTTGTCACCCTACGGAGTTTGACTTTTATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaacaaccgtgtttacactgactaacttcgacatcacatccttcgtattttagGGACTGTTGTGGACTCGAAGATTTGTCACCCTACGGAGTTTGACTTTTATCTTTGCAGTCATGCTGGAATTCAG
gactaac putative branch site (score: 1)
catccttc putative PPT
tatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcagtcattattttcgtagaatacattgctttatttatctgcttatatggaagtcattttctttggcattctcaacctgtgagactgcggtatggtgttgttggacgcgttgctgtaacaaccgtgtttacactgactaacttcgacatcacatccttcgtattttagGGACTGTTGTGGACTCGAAGATTTGTCACCCTACGGAGTTTGACTTTTATCTTTGCAGTCATGCTGGAATTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA