Sequence
atgc intronic sequence ATGC exonic sequencegtacgtcattctgaacccctcctcagatgctgggctttattctgaacataatctgcccaaaaaaatcgtccttcgcctcatttcgaaacaaaaattccagttcgacattatttatttatttcttctccgacctttgtatttgcagATGGCCGACCCTTTGACTGCTCTAATGCACGCAGTTCAGGTGATGAACTTCCTAAAGACGCTGATTCTAAGAACTTTGAAAGGTAGGGAAGAGGCGATAC
Basic information
species | Physcomitrella patens |
transcript | PP1S256_73V6.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S256_73V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os04g48790.1 (Oryza sativa), 3'ss of exon 4
gtacgtcattctgaacccctcctcagatgctgggctttattctgaacataatctgcccaaaaaaatcgtccttcgcctcatttcgaaacaaaaattccagttcgacattatttatttatttcttctccgacctttgtatttgcagATGGCCGACCCTTTGACTGCTCTAATGCACGCAGTTCAGGTGATGAACTTCCTAAAGACGCTGATTCTAAGAACTTTGAAAGGTAGGGAAGAGGCGATAC
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--------------------------------------------------------gtattagaaacaactctggattc-tttcgttagaaaagcat-------acac-atacactaac-----ctgcaatgtttgt-tttccagATGGCCGATCCATTGACTGCCCTGATACATGCAGTTCAGGTCATGAATTTCCTCAAGACATTGATCTTGAAGACTTTAAAGGAAAGAGAGGCAGCCGGAA
upper sequence: PP1S256_73V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA11G18900.1 (Glycine max), 3'ss of exon 6
gtacgtcattctgaacccctcctcagatgctgggctttattctgaacataatctgcccaaaaaaatcgtccttcgcctcatttcgaaacaaaaattccagttcgacattatttatttatttcttctccgacctttgtatttgcagATGGCCGACCCTTTGACTGCTCTAATGCACGCAGTTCAGGTGATGAACTTCCTAAAGACGCTGATTCTAAGAACTTTGAAAGGTAGGGAAGAGGCGATAC
| | | || ||| | | || | || | | || | | | || | | |||| | ||||||||||| || ||||||||||| | ||| | |||||||| ||||||||||||||||||| || || |||| || || || || | || |
-------------------------------------------gtgccatttttgtccatagag--tagtgaagatgccaatgtgatatagttgatctatcttatggtaggtttcagttacagaatttagtctttctggttgcagATGGCAGATCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTAAAGAATCTTATATTAAGGACACTGCGAGAGAGAAAGGATTGTGTGG
upper sequence: PP1S256_73V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA12G09560.1 (Glycine max), 3'ss of exon 5
gtacgtcattctgaacccctcctcagatgctgggctttattctgaacataatctgcccaaaaaaatcgtccttcgcctcatttcgaaacaaaaattccagttcgacattatttatttatttcttctccgacctttgtatttgcagATGGCCGACCCTTTGACTGCTCTAATGCACGCAGTTCAGGTGATGAACTTCCTAAAGACGCTGATTCTAAGAACTTTGAAAGGTAGGGAAGAG-GCGATAC
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-------------------------------------------gtgccatttttgtccatagag--tagtgaagatgccaatgtgatacagttgatctatcttatggttggtttcagttacagaatttagtctttttggttgcagATGGCAGACCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTGAAGAATCTTATATTAAGGACCCTGCGAGAAAGAAAGTATTGTGTCG-
upper sequence: PP1S256_73V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA03G42090.1 (Glycine max), 3'ss of exon 4
gtacgtcattctgaacccctcctcagatgctgggctttattctgaacataatctgcccaaaaaaatcgtccttcgcctcatttcgaaacaaaaattccagttcgacattatttatttatttcttctccgacctttgta-tttgcagATGGCCGACCCTTTGACTGCTCTAATGCACGCAGTTCAGGTGATGAACTTCCTAAAGACGCTGATTCTAAGAACTTTGAAAGGTAGGGAAGAGGCGATAC
||| ||| | || | | || | || || | | ||| | || | | | | |||||| | ||| || | |||| |||||||||||| |||||||||||||| | || || ||||| || ||||||||||| || ||||| ||||||| | || | || || || | | ||
-----------------------------------tttcttcctacca--gtgaggcccgtataactgtttgtatgcacatgtt---acttatgctagtggatgtggatatttaaatgtttgttt------cattgtgctttgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTGATGAACTTTCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATAAATCAATTG
upper sequence: PP1S256_73V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
gtacgtcattctgaacccctcctcagatgctgggctttattctgaacataatctgcccaaaaaaatcgtccttcgcctcat--ttcgaaacaaaaattccagttcgacattatttatttatttcttctccgacctttgtatttgcagATGGCCGACCCTTTGACTGCTCTAATGCACGCAGTTCAGGTGATGAACTTCCTAAAGACGCTGATTCTAAGAACTTTGAAAGGTAGGGAAGAGGCGATAC
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-----------------------------------------gttgatattaaat-cttgaaaatttcttgttttagctaatgctttggtccatggatttcaat---aaataga--actccttttttgtttgatttcac------cagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGGMapped 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|162255569|gb|FC431359.1|FC431359EST: AGATGAACGCTCACAACATTGCAATGGTATTTGCTCCTAACATGACCCAG ATGGCCGACCCTTTGACTGCTCTAATGCACGCAGTTCAGGTGATGAACTTC
genomic: AGATGAACGCTCACAACATTGCAATGGTATTTGCTCCTAACATGACCCAGgtacgtcatt ... gtatttgcagATGGCCGACCCTTTGACTGCTCTAATGCACGCAGTTCAGGTGATGAACTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaattccagttcgacattatttatttatttcttctccgacctttgtatttgcagATGGCCGACCCTTTGACTGCTCTAATGCACGCAGTTCAGGTGATGAACTTCCTAAAGACGCTGATTCTAAGAACTTTGAAAGGTAGGGAAGAGGCGATAC
cctttgt CT-rich tract
acattatttatttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtcattctgaacccctcctcagatgctgggctttattctgaacataatctgcccaaaaaaatcgtccttcgcctcatttcgaaacaaaaattccagttcgacattatttatttatttcttctccgacctttgtatttgcagATGGCCGACCCTTTGACTGCTCTAATGCACGCAGTTCAGGTGATGAACTTCCTAAAGACGCTGATTCTAAGAACTTTGAAAGGTAGGGAAGAGGCGATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG