Sequence
atgc intronic sequence ATGC exonic sequencegtaagatttgaaaagcacatgacaactaatctgatagaatatttatagtctctgttgtgagcaatttcaagggagtctatttcaactgtaagaatagggcttataattagccccctgctttcctcacttgatatttgaatactaatggaatcaatttacgtgatacgctcaccagGTTGTGACATTGGAAGACGTTGTTGAAGAAATTGTTGGTGAAATTTTTGATGAAAATGATTCGAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S58_81V6.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S58_81V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G153928_T03 (Zea mays), 3'ss of exon 3
gtaagatttgaaaagcacatgacaactaatctgatagaatatttatagtctctgttgtgagcaatttcaagggagtctatttcaactgtaagaatagggcttataattagccccctgctttcctcacttgatatttgaatactaatggaatcaatttacgtgatacgctcaccag-
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-----------------------------------------------------------------------------tattgcgtttagaaaatgtttatgcacagtttgtaatttcgtatgttta-tcactgcatggacacta--ggaattacttgctgaattttgtcaaaaaatgcagATTTAACATTAGAAGACGTAGTGGAAGAAATAGTTGGTGAAATCTTCGATGAGAATGATTCCAAG
upper sequence: PP1S58_81V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 10
gtaagatttgaaaagcacatgacaactaatctgatagaatatttatagtctctgttgtgagcaatttcaagggagtctatttcaactgtaagaatagggcttataattagccccctgctttcctcacttgatatttgaatactaatggaatcaatttacgtgatacgctcaccagGTTGTGACATTGGAAGACGTTGTTGAAGAAATTGTTGGTGAAATTTTTGATGAAAATGATTCGAAG
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-----------------------------------------------------------tccaagtcttctgaaatccattcc--ttgtaatct----gcttataagt----tctaacaattttcagtttat---caaatataaatgtctt--attgatattgc-catctaacagATTGTAACTCTTGAAGATGTTGTTGAGGAAATTGTTGGTGAAATCTTTGATGAAAATGACTCAAAG
upper sequence: PP1S58_81V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 10
gtaagatttgaaaagcacatgacaactaatctgatagaatatttatagtctctgttgtgagcaatttcaagggagtctatttcaactgtaagaatagggcttataattagccccctgctttcctcacttgatatttgaatactaatggaatcaatttacgtgatacgctcaccagGTTGTGACATTGGAAGACGTTGTTGAAGAAATTGTTGGTGAAATTTTTGATGAAAATGATTCGAAG
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-----------------------------------------------------------tccaagtcttctgaaatccattcca--tgtaatct----gcttataagtt-ctaacaactttcagtttatcaaatctagatgtctt---attgattttgc------catctaacagATTGTAACACTCGAAGATGTTGTTGAGGAAATTGTTGGTGAAATATTTGATGAAAATGACTCAAAG
upper sequence: PP1S58_81V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaagatttgaaaagcacatgacaactaatctgatagaatatttatagtctctgttgtgagcaatttcaagggagtctatttcaactgtaagaatagggcttataattagccccct-gctttcctcacttgatatttgaatactaatggaatcaatttacgtgatacgctcaccagGTTGTGACATTGGAAGACGTTGTTGAAGAAATTGTTGGTGAAATTTTTGATGAAAATGATTCGAAG
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---------------------------------------------------------------------------------------gtatgtgccgctcttcttttgtgcttctttactctctctcttccacagttagctaatc-tctttcctactaatttgtt----tctgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATTTTTGATGAAAACGATTCCAAA
upper sequence: PP1S58_81V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaagatttgaaaagcacatgacaactaatctgatagaatatttatagtctctgttgtgagcaatttcaagggagtctatttcaactgtaagaatagggcttataattagccccctgctttcctcacttgatatttgaatactaatggaatcaatttacgtgatacgctcaccagGTTGTGACATTGGAAGACGTTGTTGAAGAAATTGTTGGTGAAATTTTTGATGAAAATGATTCGAAG
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-------------------------------------------------------------------------------------------gtatgttgctggttgtcctcttctttactttattttttctctcctgctctcttgaaaggttgtctaattt--ctctccatgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATATTTGATGAAAACGATTCAAAG
upper sequence: PP1S58_81V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ38618 (Selaginella moellendorffii), 3'ss of exon 10
gtaagatttgaaaagcacatgacaactaatctgatagaatatttatagtctctgttgtgagcaatttcaagggagtctatttcaactgtaagaatagggcttataattagccccctgctttcctcacttgatatttgaatactaatggaatcaatttacgtgatacgctcaccagGTTGTGACATTGGAAGACGTTGTTGAAGAAATTGTTGGTGAAATTTTTGATGAAAATGATTCGAAG
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---------------------------------------------------------------------------------------------------------gtacgtttcatatcttcgtagttc--ttttcggg----agtataatacacttctattg---------cagATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAG
upper sequence: PP1S58_81V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ31527 (Selaginella moellendorffii), 3'ss of exon 10
gtaagatttgaaaagcacatgacaactaatctgatagaatatttatagtctctgttgtgagcaatttcaagggagtctatttcaactgtaagaatagggcttataattagccccctgctttcctcacttgatatttgaatactaatggaatcaatttacgtgatacgctcaccagGTTGTGACATTGGAAGACGTTGTTGAAGAAATTGTTGGTGAAATTTTTGATGAAAATGATTCGAAG
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-----------------------------------------------------------------------------------------------------------------------------gtacgtttcatagttcttttcgggagta--taatacacttctattgc-agATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAGMapped 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|162197605|gb|FC374439.1|FC374439EST: GTAAAGTACACATGGCCATCGTGCTCAATGAATATGGTGGCACTGTCGGA GTAGTGACATTGGAAGACGTTGTTGAAGAAATTGTTGGTGAAATTTTTGAT
genomic: GTAAAGTACACATGGCCATCGTGCTCAATGAATATGGTGGCACTGTCGGAgtaagatttg ... cgctcaccagGTTGTGACATTGGAAGACGTTGTTGAAGAAATTGTTGGTGAAATTTTTGAT
EST:
gi|22492136|gb|BU052059.1|BU052059EST: GTAAAGTACACATGGCCATCGTGCTCAATGAATATGGTGGCACTGTCGGA GTTGTGACATTGGAAGACGTTGTTGAAGAAATTGTTGGTGAAATTTTTGAT
genomic: GTAAAGTACACATGGCCATCGTGCTCAATGAATATGGTGGCACTGTCGGAgtaagatttg ... cgctcaccagGTTGTGACATTGGAAGACGTTGTTGAAGAAATTGTTGGTGAAATTTTTGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctcacttgatatttgaatactaatggaatcaatttacgtgatacgctcaccagGTTGTGACATTGGAAGACGTTGTTGAAGAAATTGTTGGTGAAATTTTTGATGAAAATGATTCGAAG
tactaat putative branch site (score: 1)
atatttgaatactaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatttgaaaagcacatgacaactaatctgatagaatatttatagtctctgttgtgagcaatttcaagggagtctatttcaactgtaagaatagggcttataattagccccctgctttcctcacttgatatttgaatactaatggaatcaatttacgtgatacgctcaccagGTTGTGACATTGGAAGACGTTGTTGAAGAAATTGTTGGTGAAATTTTTGATGAAAATGATTCGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA