Sequence
atgc intronic sequence ATGC exonic sequencegtaagtggaacatgggacgtagtgtattagggttatttgtaggtgcgaattggtttcttaggattcagtgatagtctgccgatcttgaatttctggtttgtttttttcgttactgagttgattgagggagcactgtgcgtgcatttttggtgggtagagttggaagctgttgaacgttatatgggtgttttacagGCGACCATGGTCTGCATGGACAACTCAGAGTGGATGCGGAACGGCGATTATTCACCTACTAGGTTTCAAGCTCAAGCTGATGCTATAAACCTGATTTGCG
Basic information
species | Physcomitrella patens |
transcript | PP1S14_318V6.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S14_318V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 1
gtaagtggaacatgggacgtagtgtattagggttatttgtaggtgcgaattggtttcttaggattcagtgatagtctgccgatcttgaatttctggtttgtttttttcgttactgagttgattgagggagcactgtg-cgtgcatttttggtgggtagagttggaagctgttgaacgttatatgggtgttttacagGCGACCATGGTCTGCATGGACAACTCAGAGTGGATGCGGAACGGCGATTATTCACCTACTAGGTTTCAAGCTCAAGCTGATGCTATAAACCTGATTTGCG
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-----------------------------------------------------------------------------------------------gttcgccgcgcagctcgccgccctccctcccacagatcgatttcgccgagctctgattcacttatttatcgctttttttgcgtggctcccct-ctccgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTACTCGCCGTCGCGATTCCAGGCTCAGGCCGACGCCGTCAACCTCATCTGTG
upper sequence: PP1S14_318V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G147671_T02 (Zea mays), 3'ss of exon 1
gtaagtggaacatgggacgtagtgtattagggttatttgtaggtgcgaattggtttcttaggattcagtgatagtctgccgatcttgaatttctggtttgtttttttcgttactgagttgattgagggagcactgtgcgtgcatttttggtgggtagagttggaagctgttgaacgttatatgggtgttttacagGCGACCATGGTCTGCATGGACAACTCAGAGTGGATGCGGAACGGCGATTATTCACCTACTAGGTTTCAAGCTCAAGCTGATGCTATAAACCTGATTTGCG
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--------------------------------------------------------------------------------------------------------gtacgacatgcgccctgctgccgtttctcgctccgtgaactcgatccccaactaatctcctcccctcgattggctt-----tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTACGCCCCGTCGCGGTTCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCG
upper sequence: PP1S14_318V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G039577_T03 (Zea mays), 3'ss of exon 1
gtaagtggaacatgggacgtagtgtattagggttatttgtaggtgcgaattggtttcttaggattcagtgatagtctgccgatcttgaatttctggtttgtttttttcgttactgagttgattgaggg-agcactgtgcgtgcatttttggtgggtagagttggaagctgttgaacgttatatgggtgttttacagGCGACCATGGTCTGCATGGACAACTCAGAGTGGATGCGGAACGGCGATTATTCACCTACTAGGTTTCAAGCTCAAGCTGATGCTATAAACCTGATTTGCG
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----------------------------------------------------gtccatatgcatcccctccttccttcctcttccttc-tatctgctatggctgctgccccaccggtctaatgacgcgcagcgatttctgaccatcccctgacggtttg--cggtggccgtccaaatccaa---------tcccagGCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTATCCCCCATCGCGGTTCGCGGCGCAGGCCCACGCCTTCGCCGTCCTCTCCG
upper sequence: PP1S14_318V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtggaacatgggacgtagtgtattagggttatttgtaggtgcgaattggtttcttaggattcagtgatagtctgccgatcttg--aatttctggtttgtttttttcgttactgagttgattgagggagcactgtgcgtgcatttttggtgggtagagttggaagctgttgaacgttatatgggtgttttacagGCGACCATGGTCTGCATGGACAACTCAGAGTGGATGCGGAACGGCGATTATTCACCTACTAGGTTTCAAGCTCAAGCTGATGCTATAAACCTGATTTGCG
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-------------------------------------------------------------------------gtatgcctatcctatttacttccacttttgccattctatttcctaat-atttatactctttttcttctttcacaaatta-gggttttctcaccgattattttaatttgcatcattctgattcagGCGACTATGATCTGTATCGACAATTCCGAATGGATGCGAAATGGCGATTATTCTCCCACTAGATTTCAGGCTCAAGCCGACGCCGTTAATCTTATCTGTGMapped 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|18328677|gb|BJ160682.1|BJ160682EST: TTGAGTGCTTCTTTGATGGAGTCCGGTGGTCATCACTGCGATGATGCCGT GCGACCATGGTCTGCATGGACAACTCAGAGTGGATGCGGAACGGCGATTAT
genomic: TTGAGTGCTTCTTTGATGGAGTCCGGTGGTCATCACTGCGATGATGCCGTgtaagtggaa ... tgttttacagGCGACCATGGTCTGCATGGACAACTCAGAGTGGATGCGGAACGGCGATTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatttttggtgggtagagttggaagctgttgaacgttatatgggtgttttacagGCGACCATGGTCTGCATGGACAACTCAGAGTGGATGCGGAACGGCGATTATTCACCTACTAGGTTTCAAGCTCAAGCTGATGCTATAAACCTGATTTGCG
ttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtggaacatgggacgtagtgtattagggttatttgtaggtgcgaattggtttcttaggattcagtgatagtctgccgatcttgaatttctggtttgtttttttcgttactgagttgattgagggagcactgtgcgtgcatttttggtgggtagagttggaagctgttgaacgttatatgggtgttttacagGCGACCATGGTCTGCATGGACAACTCAGAGTGGATGCGGAACGGCGATTATTCACCTACTAGGTTTCAAGCTCAAGCTGATGCTATAAACCTGATTTGCG
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