Sequence
atgc intronic sequence ATGC exonic sequencegtacgttgtttgagaccatgtttatccgtccgttccatggttcagctgtcattgtagtagtcactcgcgagttttattacagtcgtcactcacagtgcatctttctgtgtttagctgttctctattttgaaaccatcacttgaaagtgctgagaggagttcatctcgttctgttttctgcagTGCGATCAGCGAAGTTTATCCCCCGTAAGCAGTGGGTTGTGGCTTGCTCTGATGACATGTTCATCCGAGTGTATAACTATAACACGATGGACAAAGTGAA
Basic information
species | Physcomitrella patens |
transcript | PP1S79_180V6.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 5
gtacgttgtttgagaccatgtttatccgtccgttccatggttcagctgtcattgtagtagtcactcgcgagttttattacagtcgtcactcacagtgcatctttctgtgtttagctgttctctattttgaaaccatcacttgaaagtgctgagaggagttcatctcgttctgttttctgcagTGCGATCAGCGAAGTTTATCCCCCGTAAGCAGTGGGTTGTGGCTTGCTCTGATGACATGTTCATCCGAGTGTATAACTATAACACGATGGACAAAGTGAA
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-------------------------------------------------------------------------------------gtatgctcacc-caactttctgtgtgc-----ttcttgtccgtgaggt--ttacttca---tgctaa--------tattcaataacaatttc---agTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGATGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G443953_T01 (Zea mays), 3'ss of exon 6
gtacgttgtttgagaccatgtttatccgtccgttccatggttcagctgtcattgtagtagtcactcgcgagttttattacagtcgtcactcacagtgcatctttctgtgtttagctgttctctattttgaaaccatcacttgaaagtgctgagaggagttcatctcgttctgttttctgcagTGCGATCAGCGAAGTTTATCCCCCGTAAGCAGTGGGTTGTGGCTTGCTCTGATGACATGTTCATCCGAGTGTATAACTATAACACGATGGACAAAGTGAA
|||| | | | | || ||| || || |||| | || | |||| ||| | | | || || | | |||| | |||| |||||| || || || || ||||| | | ||||| |||||||| ||| | | ||||||||||||||||| |||||||||||||| || ||||| || || ||
-------------------------------------------------------------------tgagtctaagaagactcaa-----acaa-gcccattactgtctacagtt-ttctgtat---gcatttgtgtttt-----tgtgcaattatgctcatgtaaccatgttaattgcagTTCGTTCGGCTAAATTTATTGCACAGAAGCAATGGGTTGTTGCTGGTGCCGATGACATGTTCATCCGTGTGTATAACTATAATACCATGGATAAGGTCAA
upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 5
gtacgttgtttgagaccatgtttatccgtccgttccatggttcagctgtcattgtagtagtcactcgcgagttttattacagtcgtcactcacagtgcatctttctgtgtttagctgttctctattttgaaaccatcacttgaaagtgctgagaggagttcatctcgttctgttttctgcagTGCGATCAGCGAAGTTTATCCCCCGTAAGCAGTGGGTTGTGGCTTGCTCTGATGACATGTTCATCCGAGTGTATAACTATAACACGATGGACAAAGTGAA
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--------------------------------------------------------------------------------------------------------gtatgcacaaccaattttctgcttgcttctcttcccttaggtttacatcatgctgatattccataacaatttc---agTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGACGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAAMapped 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|18345941|gb|BJ177984.1|BJ177984EST: AGCCTGGTGAAGTCTTTCGAGGTTACCGACCTGCCAG TGCGATCAGCGAAGTTTATCCCCCGTAAGCAGTGGGTTGTGGCTTGCTCTG
genomic: AGCCTGGTGAAGTCTTTCGAGGTTACCGACCTGCCAGgtacgttgtt ... ttttctgcagTGCGATCAGCGAAGTTTATCCCCCGTAAGCAGTGGGTTGTGGCTTGCTCTG
EST:
gi|18374691|gb|BJ206269.1|BJ206269EST: AGCCTGGTGAAGTCTTTCGAGGTTACCGACCTGCCAG TGCGATCAGCGAAGTTTATCCCCCGTAAGCAGTGGGTTGTGGCTTGCTCTG
genomic: AGCCTGGTGAAGTCTTTCGAGGTTACCGACCTGCCAGgtacgttgtt ... ttttctgcagTGCGATCAGCGAAGTTTATCCCCCGTAAGCAGTGGGTTGTGGCTTGCTCTG
EST:
gi|18366204|gb|BJ198282.1|BJ198282EST: AGCCTGGTGAAGTCTTTCGAGGTTACCGACCTGCCAG TGCGATCAGCGAAGTTTATCCCCCGTAAGCAGTGGGTTGTGGCTTGCTCTG
genomic: AGCCTGGTGAAGTCTTTCGAGGTTACCGACCTGCCAGgtacgttgtt ... ttttctgcagTGCGATCAGCGAAGTTTATCCCCCGTAAGCAGTGGGTTGTGGCTTGCTCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaaccatcacttgaaagtgctgagaggagttcatctcgttctgttttctgcagTGCGATCAGCGAAGTTTATCCCCCGTAAGCAGTGGGTTGTGGCTTGCTCTGATGACATGTTCATCCGAGTGTATAACTATAACACGATGGACAAAGTGAA
tctcgttctgttttct CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgttgtttgagaccatgtttatccgtccgttccatggttcagctgtcattgtagtagtcactcgcgagttttattacagtcgtcactcacagtgcatctttctgtgtttagctgttctctattttgaaaccatcacttgaaagtgctgagaggagttcatctcgttctgttttctgcagTGCGATCAGCGAAGTTTATCCCCCGTAAGCAGTGGGTTGTGGCTTGCTCTGATGACATGTTCATCCGAGTGTATAACTATAACACGATGGACAAAGTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA