Sequence
atgc intronic sequence ATGC exonic sequenceAGAACCACCCCGAGCTATGTGGCTTTCACTGACTCTGAGCGTCTCATCGGTGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagtttttcccatttctttgtcgtagctttcgtttctatccttgacaggttctatgcagcattcggttgttactctgttgtttttcgtatctcttgtg...
Basic information
species | Physcomitrella patens |
transcript | PP1S39_121V6.1 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S39_121V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os03g60620.1 (Oryza sativa), 5'ss of exon 1
AGAACCACCCCGAGCTATGTGGCTTTCACTGACTCTGAGCGTCTCATCGGTGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagtttttcc-catttctttgtcgtagctttcgtttctatccttg-acaggttctatgcagcattcggttgttactctgttgtttttcgtatctcttgtg
| |||||||| ||| || | ||||| ||| | ||||| |||||||| ||||| || ||||| ||||| |||||||||||||||||||| || |||||||||| || | |||| | | || | ||| ||| || || | | | | | | | | | | | | | | |
CGCACCACCCCCTCCTACGTCGGGTTCACGGACACCGAGCGCCTCATCGGGGATGCCGCCAAGAACCAGGTCGCCATGAACCCCATCAACACCGTCTTCGgtgagtaacgccacgacgcttttgccctgtttctgattcgatctgtgtactgttgcgactagatgtgtgatctgtgtttcgcgtaatgtgatgcccgatt--
upper sequence: PP1S39_121V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os11g47760.3 (Oryza sativa), 5'ss of exon 1
AGAACCACCCCGAGCTATGTGGCTTTCACTGACTCTGAGCGTCTCATCGGTGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagt-ttttcccatttctttgtcgtagctttcgtttctatccttgacaggttctatgcagcattcggttgttactctgttgtttttcgtatctcttgtg
| |||||||| ||| || | ||||| ||||| ||| | |||||||| |||||||| ||||| ||||| |||||||||||||||||||| || || ||| | | || | | || || | ||||| || | | || || | | | || || | | |
CGCACCACCCCCTCCTACGTCGGCTTCACCGACTCCGAGAGGCTCATCGGAGATGCTGCCAAGAACCAGGTCGCCATGAACCCCATCAACACCGTCTTTGgtaactacttattccctgctcctcagtcctctctctttctctctctccccccttagatctcatctctaaggtcttcgtcgtcgtcgtatgctagatctac-
upper sequence: PP1S39_121V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G340251_T01 (Zea mays), 5'ss of exon 2
AGAACCACCCCGAGCTATGTGGCTTTCACTGACTCTGAGCGTCTCATCGGTGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagtttttcccatttctttgtcgtagctttcgtttctatccttgacaggttctatgcagcattcggttgttactctgttgtttttcgtatctcttgtg--
| ||||| || || || || ||||| ||||| ||||| |||||||| ||||| || ||||| ||||| |||||||||||||||||||| || || ||||||| ||| || | | | | || ||| | || | ||| | | | | | | | | | | | | || | |
CGCACCACGCCCTCGTACGTCGCCTTCACCGACTCCGAGCGCCTCATCGGAGATGCGGCCAAGAACCAGGTCGCCATGAACCCCATCAACACCGTCTTTGgtgagtacactccaccatttaggctcttactcctttcctagctcggatacgttttgtttaccgt--gactagcggttttgtctgacccatacgacccatcta
upper sequence: PP1S39_121V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G056039_T01 (Zea mays), 5'ss of exon 1
AGAACCACCCCGAGCTATGTGGCTTTCACTGACTCTGAGCGTCTCATCGGTGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagtttttcccatttctttgtcgtagctttcgtttctatccttgacaggttctatgcagcattcggttgttactctgttgtttttcgtatctcttgtg-
| ||||| || || || || ||||| ||||| ||||| |||||||| ||||| || ||||| ||||| |||||||||||||||||||| || || |||||| || |||| || | | | || || | | || | | | || ||| | |||| | | ||| | | |
CGCACCACACCCTCGTACGTCGCCTTCACCGACTCCGAGCGCCTCATCGGAGATGCGGCCAAGAACCAGGTCGCCATGAACCCCATCAACACCGTCTTTGgtgagcacgccctcgttctcggttcttcttactcctgctgctctagctgagatccgttttgttcaccgtgattagt-tgtttggtctggtagatgtaccgc
upper sequence: PP1S39_121V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA03G32850.1 (Glycine max), 5'ss of exon 1
AGAACCACCCCGAGCTATGTGGCTTTCACTGACTCTGAGCGTCTCATCGGTGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagtttttcccatttctttgtcgtagctttcgtttctatccttgacaggttctatgcagcattcggttgttactctgttgtttttcgtatctcttgtg---
|||||||| ||| || || | ||||||||| | |||||||||||||||||||| || |||||||| || |||||||||||||||||||| || |||||| | | | | || | || |||| | ||| ||| |||| | || | | | | ||||| | || |
AGAACCACGCCGTCTTACGTCGGATTCACTGACACCGAGCGTCTCATCGGTGATGCGGCCAAGAATCAAGTCGCCATGAACCCCATCAACACCGTCTTCGgtaacctctcttaacaaaattattttatcttttccattcga--ttgttctgtt-tatgtattttttttatacttattttaggttttaggctaaactattcact
upper sequence: PP1S39_121V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA19G35560.1 (Glycine max), 5'ss of exon 1
AGAACCACCCCGAGCTATGTGGCTTTCACTGACTCTGAGCGTCTCATCGGTGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagtttttcccatttc--tttgtcgtagctttcgtttctatccttgacaggttctatgcagcattcggttgttactctgttgtttttcgtatctcttgtg--
||||| || ||| || || | |||||||| | |||||||||||||||||||| |||||||| || || |||||||||||||||||||| || |||||| | | | | | ||| | || ||| |||| | || | | | |||||| || || | || ||| | | |
AGAACGACGCCGTCTTACGTCGGCTTCACTGATACCGAGCGTCTCATCGGTGATGCGGCTAAGAACCAAGTCGCCATGAACCCCATCAACACCGTCTTCGgtaacctctcttaaccccaattttttttatcttctgttttagttttt--ctg--tttatgcatttttattttagttatcagttataggctaaactattcacttt
upper sequence: PP1S39_121V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA18G52650.1 (Glycine max), 5'ss of exon 1
AGAACCACCCCGAGCTATGTGGCTTTCACTGACTCTGAGCGTCTCATCGGTGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagtttttcccatt-tctttgtcgtagctttcgtttctatccttgacaggttctatgcagcattcggt-tgttactctgttgtttttcgtatctcttgtg
| ||||| || ||||| || ||||| || | || | |||||||| ||||| |||||||| ||||| |||||||||||||||||||| || |||||| | | || | | || || || | | | | | | | | ||||| ||| || | ||| | |||||| || | | ||||
CGTACCACACCCTCTTATGTCGCCTTCACCGATACCGAAAGACTCATCGGAGATGCCGCTAAGAACCAGGTCGCCATGAACCCCATCAACACCGTCTTCGgtaattcttctcagtcctcattatctgctcaataatatttttacctacatttttctaacaagctttttacattttatcgtaatgttttatgt-tttattgt-
upper sequence: PP1S39_121V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA13G19330.1 (Glycine max), 5'ss of exon 1
AGAACCACCCCGAGCTATGTGGCTTTCACTGACTCTGAGCGTCTCATCGGTGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagtttttcccatttctt-tgtcgtagctttcgt-ttctatccttgacaggttctatgcagcattcggttgttactctgttgtttttcgtatctcttgtg
||||| || ||| || || | ||||| ||| | ||||||||||| |||||||| || || |||||||| |||||||||||||||||||| || || ||| || | || ||| | | ||| | || | || || | | | | ||| | | | || |||| || || | | || |
AGAACGACGCCGTCTTACGTCGGGTTCACCGACACCGAGCGTCTCATTGGTGATGCCGCAAAAAATCAGGTCGCCATGAACCCCATCAACACCGTCTTTGgtaagatccccctgcttcaaatttagtattgtacggacacggtcttttttatgacatgtttttttttcacgt-tgatgttgctgttgttggtgtttttttt-
upper sequence: PP1S39_121V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv06s0004g04470.t01 (Vitis vinifera), 5'ss of exon 1
AGAACCACCCCGAGCTATGTGGCTTTCACTGACTCTGAGCGTCTCATCGGTGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagtttttcccatttctttgtcg-tagctttcgtttctatccttgacaggttctatgcagcattcggttgttactctgttgtttttcgtatctcttgtg------
|| || || || |||||| |||||||||||| | |||||| | |||||||||||||| ||||| ||||| ||||||||||| || |||||||| || ||| || | | | ||| ||||| | | |||| | | || ||| || || || || | || | | | | |
AGGACTACGCCTTCCTATGTTGCTTTCACTGACACGGAGCGTTTGATCGGTGATGCTGCCAAGAACCAGGTCGCCATGAACCCTATAAACACTGTTTTTGgtaagcctatggc---tctctgtcgattgacagtgttttttttttttt----ttcaatttgagttttagtgatttgtttggttgctaagaaagttgaggaaaaagaa
upper sequence: PP1S39_121V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv06s0004g04510.t01 (Vitis vinifera), 5'ss of exon 1
AGAACCACCCCGAGCTATGTGGCTTTCACTGACTCTGAGCGTCTCATCGGTGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagtttttcccatttctttgtcgtagcttt-cgtttctatccttgacaggttctatgcagcattcggttgttactctgttgtttttcgtatctcttgtg------
|| || || || || || |||||||| || | |||||| | ||||||||||| || ||||||||||| || ||||||||||| |||||||| |||||||||| | ||||| | | | | | | | | | || || | || | | | ||| || | |||| || || | ||| | |
AGGACTACTCCCTCTTACGTTGCTTTCACCGATACAGAGCGTTTGATCGGTGATGCCGCCAAGAATCAGGTCGCTATGAACCCCATTAACACTGTTTTCGgtgagtcatc----tttctctatactggatctgcaatacaatgttttttattttattt-tattattatgtca--gatttgttattatttttgtctttgttcaagatt
upper sequence: PP1S39_121V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv08s0007g00130.t01 (Vitis vinifera), 5'ss of exon 1
AGAACCACCCCGAGCTATGTGGCTTTCACTGACTCTGAGCGTCTCATCGGTGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagtttttcccatttctttgtcgtagctttcgtttctatccttgacaggttctatgcagcattcggttgttactctgttgtt-tttcgtatctcttgtg-
|| || || ||| ||||| || |||||||| | ||| | | |||||||||| |||||||| ||||| |||||||||||||| ||||| || || ||| || | | | | ||| ||| | | | |||| | |||| | | ||||||| | || | |||| | || | | | ||
AGGACGACGCCGTCTTATGTTGCGTTCACTGATACCGAGAGGTTGGTCGGTGATGCAGCTAAGAACCAGGTCGCCATGAACCCCATTAACACCGTCTTTGgtaagatcctact-tctctcattcggaattatggttttcacttttga-atctgtaatgcagctctaaatttgtttctgattgtgatcatgtttttatagttt
upper sequence: PP1S39_121V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv13s0019g01430.t01 (Vitis vinifera), 5'ss of exon 1
AGAACCACCCCGAGCTATGTGGCTTTCACTGACTCTGAGCGTCTCATCGGTGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagtttttcccattt--ctttgtcgtagctttcgtttctatccttgacaggttctatgcagcattcggttgttactctgttgtttttcgtatctcttgtg
||||| || ||| || || ||||||||||| | || | || ||||| ||||| || ||||| ||||| || |||||||| ||||||||||| |||||| |||||| || | ||||| | | ||| || | || | | | || | ||| | ||| | ||| | || || |
AGAACGACGCCGTCTTACGTTGCTTTCACTGATACGGAAAGGCTGATCGGAGATGCGGCCAAGAACCAGGTTGCGATGAACCCGATCAACACTGTTTTCGgtatgtttttaagatctagttttgttttggtttttgtggttccgactggatcttgtattagaagctttgtttgccattctttgatttataagatttcgtt--
upper sequence: PP1S39_121V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ11703 (Selaginella moellendorffii), 5'ss of exon 1
AGAACCACCCCGAGCTATGTGGCTTTCACTGACTCTGAGCGTCTCATCGGTGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagtttttcccatttct--ttgtcgtagctttcgtttctatccttgacaggttctatgcagcattcgg--ttgttactctgttgttt--ttcgtatctcttgtg-----------------------------------
|| || || || |||||||| ||||| ||| | ||||| |||||||| ||||| || ||||| ||||| |||||||| |||||||||||||| ||||||||||| | | ||| | ||| | | || |||| | | ||| ||| | |||| | | ||| | | | | |||| ||
AGGACGACGCCATCGTATGTGGCCTTCACCGACACGGAGCGGCTCATCGGCGATGCCGCGAAGAACCAGGTCGCCATGAATCCCATCAACACTGTCTTCGgtgagttcctagtagatctagctctcgaaaatcgcggctctaggatcta---gtttcatgtttccttcgaaatcttagatctaggatctagcttgcatctaacttgcccgagatagctgaaagttgagctttttcttccag
upper sequence: PP1S39_121V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ22479 (Selaginella moellendorffii), 5'ss of exon 1
AGAACCACCCCGAGCTATGTGGCTTTCACTGACTCTGAGCGTCTCATCGGTGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagtttttcccatttct--ttgtcgtagctttcgtttctatccttgacaggttctatgcagcattcgg--ttgttactctgttgttt--ttcgtatctcttgtg-----------------------------------------------
|| || || || |||||||| ||||| ||| | ||||| |||||||| ||||| || ||||| ||||| |||||||| |||||||||||||| ||||||||||| | | ||| | ||| | | || ||| | | ||| ||| | |||| | | ||| | | | | |||| ||
AGGACGACGCCATCGTATGTGGCCTTCACCGACACGGAGCGGCTCATCGGCGATGCCGCGAAGAACCAGGTCGCCATGAATCCCATCAACACTGTCTTCGgtgagttcctagtagatctagctctcgaaaatcgcggctctgggatcta---gtttcatgtttccttcgaaatcttagatctaggatctagcttgcatctaacttgcccgagatacttgtttctttagctgaaagttgagctttttcttccagMapped 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|18361752|gb|BJ193819.1|BJ193819EST: TGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCG ATGCTAAGAGGTTAATTGGAAGGCGTTTTAGTGACGCTTCTGTCCAGAGTG
genomic: TGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagttttt ... gacaatgtagATGCTAAGAGGTTAATTGGAAGGCGTTTTAGTGACGCTTCTGTCCAGAGTG
EST:
gi|18331892|gb|BJ163904.1|BJ163904EST: TGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCG ATGCTAAGAGGTTAATTGGAAGGCGTTTTAGTGACGCTTCTGTCCAGAGTG
genomic: TGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagttttt ... gacaatgtagATGCTAAGAGGTTAATTGGAAGGCGTTTTAGTGACGCTTCTGTCCAGAGTG
EST:
gi|100408275|gb|BY955953.1|BY955953EST: TGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCG ATGCTAAGAGGTTAATTGGAAGGCGTTTTAGTGACGCTTCTGTCCAGAGTG
genomic: TGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagttttt ... gacaatgtagATGCTAAGAGGTTAATTGGAAGGCGTTTTAGTGACGCTTCTGTCCAGAGTG
EST:
gi|208390597|gb|DC937529.1|DC937529EST: TGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCG ATGCTAAGAGGTTAATTGGAAGGCGTTTTAGTGACGCTTCTGTCCAGAGTG
genomic: TGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagttttt ... gacaatgtagATGCTAAGAGGTTAATTGGAAGGCGTTTTAGTGACGCTTCTGTCCAGAGTG
EST:
gi|100404749|gb|BY991264.1|BY991264EST: TGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCG ATGCTAAGAGGTTAATTGGAAGGCGTTTTAGTGACGCTTCTGTCCAGAGTG
genomic: TGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagttttt ... gacaatgtagATGCTAAGAGGTTAATTGGAAGGCGTTTTAGTGACGCTTCTGTCCAGAGTG
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
31 (upstream exon),
34 (downstream exon)
Score:
10AGAACCACCCCGAGCTATGTGGCTTTCACTGACTCTGAGCGTCTCATCGGTGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagttttt ... gacaatgtagATGCTAAGAGGTTAATTGGAAGGCGTTTTAGTGACGCTTCTGTCCAGAGTGATATGAAGTTGTGGCCATTCAAGATCACCCCCGGGCCGGGAGAGAAGCC
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGAACCACCCCGAGCTATGTGGCTTTCACTGACTCTGAGCGTCTCATCGGTGATGCTGCTAAGAATCAGGTGGCCATGAACCCCATCAACACTGTATTCGgtgagtttttcccatttctttgtcgtagctttcgtttctatccttgacaggttctatgcagcattcggttgttactctgttgtttttcgtatctcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT