Sequence
atgc intronic sequence ATGC exonic sequencegtactacctcttttcatctgcacttggttcagttcttccatattaaagtggttacaggagttacgcttttgttttgttgattaacctccaaaactgctaacgttgttgttgtggtggctactttgtggaccattatctttgcagCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTTAGCGAGGGTACTAGTGCAGATCGAGAAATCCAGCGTACCCTTATGGAGT
Basic information
species | Physcomitrella patens |
transcript | PP1S13_419V6.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S13_419V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G074037_T01 (Zea mays), 3'ss of exon 6
gtactacctcttttcatctgcacttggttcagttcttccatattaaagtggttacaggagttacgcttttgttttgttgattaacctccaaaac---tgctaacgttgttgttgtggtggctactttgtggaccattatctttgc--agCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTTAGCGAGGGTACTAGTGCAGATCGAGAAATCCAGCGTACCCTTATGGAGT
| | || | || | || ||| | | || || || | || ||| | | | | | ||| | | |||| |||| |||||||| || |||||||| |||||||||||||| ||||| | ||||| ||||| || ||||||||||| || || ||| | || | ||||||
-------------------------------------------------acacccgtggcccgtgcataatttcttttaattgaagtgcataatccgtgtatatgtcattgctataaaatgttgtctttggttttatcttgttgcctagCCATGCATCATTTTCATGGATGAAATTGATGCCATTGGTGGCCGAAGATTTAGTGAGGGCACAAGTGCAGATCGTGAGATTCAGAGGACATTGATGGAGC
upper sequence: PP1S13_419V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G171604_T01 (Zea mays), 3'ss of exon 6
gtactacctcttttcatctgcacttggttcagttcttccatattaaagtggttacaggagttacgcttttgttttgttgattaacctccaaaactgctaacgttgttgttgt-ggtggctactttgtggaccattatctttgcagCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTTAGCGAGGGTACTAGTGCAGATCGAGAAATCCAGCGTACCCTTATGGAGT
|| | || | || || ||| | | | | | | | | | || | | || | ||| | | ||| |||| |||||||| || |||||||| |||||||||||||| || || | || || ||||| |||||||| ||||| || |||||||| || | |||||
---------------------------------------------aatcactaacgcacttcccgtacctgccgtgtaccatcatccgttttagttccatcactaatgatattagtttttttcatgtcaaattgttcttttctagCCATGCATCATCTTCATGGATGAAATTGATGCCATTGGTGGGCGAAGATTCAGTGAGGGAACTAGTGCTGATCGTGAGATCCAGCGGACGTTGATGGAAC
upper sequence: PP1S13_419V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA04G03180.1 (Glycine max), 3'ss of exon 6
gtactacctcttttcatctgcacttggttcagttcttccatattaaagtggttacaggagttacgcttttgttttgttgattaacctccaaaactgctaacgttgttgttgtggtggctactttgtggaccattatctttgcagCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTTAGCGAGGGTACTAGTGCAGATCGAGAAATCCAGCGTACCCTTATGGAGT
| | | || ||| ||| | ||| | | | | | | | || | | || |||| | ||||||||||||| |||||||||||||| |||||||||||||| || ||||| || ||||| || ||||||||||| || || ||| | || || ||||||
---------------------------------------------------------gtgagataattgtgtgaaattgtctt-cctataggtttacacatactaattgaaagatgttctaaatctatac-attacttgattagCCTTGCATCATTTTTATGGATGAGATCGATGCCATTGGAGGTCGCCGTTTCAGTGAGGGAACAAGTGCAGATCGTGAGATTCAGAGAACGCTAATGGAGC
upper sequence: PP1S13_419V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA17G37220.1 (Glycine max), 3'ss of exon 6
gtactacctcttttcatctgcacttggttcagttcttccatattaaagtggttacaggagttacgcttttgttttgttgattaacctccaaaactgctaacgttgttgttgtggtggctactttgtggaccattatctttgcagCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTTAGCGAGGGTACTAGTGCAGATCGAGAAATCCAGCGTACCCTTATGGAGT
|| | | || | | | | || | || || | | ||| | || |||||| | | | | ||||| ||| ||||||||||||| |||||||||||||| ||||||||||| || |||||||| || ||||| || ||||| ||||| || || ||| | || || ||||||
----------------------------------------------ggtagattattgaatgaagttctt--cctatttgttcatatattaaatgg--aatgttgttctga--atctccattttgt---ttgtta-------aGCCTTGCATCATTTTTATGGATGAGATCGATGCCATTGGTGGTCGTCGTTTCAGTGAGGGAACAAGTGCTGATCGTGAGATTCAGAGAACACTAATGGAG-
upper sequence: PP1S13_419V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA14G07750.1 (Glycine max), 3'ss of exon 6
gtactacctcttttcatctgcacttggttcagttcttccatattaaagtggttacaggagttacgcttttgttttgttgattaacctccaaaactgctaacgt-tgttgttgtggtggctactttgtggac--cattatctttgc--agCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTTAGCGAGGGTACTAGTGCAGATCGAGAAATCCAGCGTACCCTTATGGAGT
|| |||| || | || | | | || ||| | || | | |||| | |||| ||||||||||||| |||||||||||||| ||||||||||| || |||||||| || ||||| || ||||| ||||| || || ||| | || || |||||||
---------------------------------------------------------------------------gtagattcttgaatgaagtttctttcatatattaaaatggaatatggttctgagtctccattttgtttgttaagCCTTGCATCATTTTTATGGATGAGATCGATGCCATTGGTGGTCGTCGTTTCAGTGAGGGAACAAGTGCTGATCGTGAGATTCAGAGAACACTAATGGAGT
upper sequence: PP1S13_419V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA06G03230.1 (Glycine max), 3'ss of exon 6
gtactacctcttttcatctgcacttggttcagttcttccatattaaagtggttacaggagttacgcttttgttttgttgattaacctccaaaactgctaacgttgttgttgtggtggctactttgtggaccattatctttgcagCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTTAGCGAGGGTACTAGTGCAGATCGAGAAATCCAGCGTACCCTTATGGAGT
| | | |||| ||| ||| | ||| | | | | | | | | || | | || || | | |||| |||||||| |||||||||||||| |||||||||||||| || ||||| || ||||| || ||||||||||| || || ||| | || || ||||||
---------------------------------------------------------gtgagatgcttgtgtgaaattgtctt-cctataggtttacacatactaatttaaagatgttctaaatctatacttttcttgat-tagCCGTGCATCATTTTTATGGATGAGATCGATGCCATTGGAGGTCGCCGTTTCAGTGAGGGAACAAGTGCAGATCGTGAGATTCAGAGAACGCTAATGGAGC
upper sequence: PP1S13_419V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA06G01200.1 (Glycine max), 3'ss of exon 8
gtactacctcttttcatctgcacttggttcagttcttccatattaaagtggttacaggagttacgcttttgttttgttgattaacctccaaaactgctaacgttgttgttgtggtggctactttgtggaccattatctttgc--agCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTTAGCGAGGGTACTAGTGCAGATCGAGAAATCCAGCGTACCCTTATGGAGT
| || | ||| ||| ||| | | | | |||| | || | | |||| | |||| |||||||||||||||| |||||||||||||||||||||| || || |||| || | | | || | ||||| ||||| || | ||||| | ||||
---------------------------------------------------------gtattgagaacttgcattgcatcaaaacaggatttttttttcatgcccttgtagaattgatttttactatttccatcctttttgtttagCCTTGCATCATATTCATGGATGAGATTGATGCCATTGCTGGACGACGTTCCAGTAACCGCAAAGGTTCTGATCGTGAAATTCAAAGAACCCTCAAGGAGC
upper sequence: PP1S13_419V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv03s0038g04350.t01 (Vitis vinifera), 3'ss of exon 6
gtactacctcttttcatctgcacttggttcagttcttccatattaaagtggttacaggagttacgcttttgttttgttgattaacctccaaaactgctaacgttgttgttgtggtggctactttgtggaccattatctttgcagCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTTAGCGAGGGTACTAGTGCAGATCGAGAAATCCAGCGTACCCTTATGGAGT
|| | || || | | |||| | |||| | ||| | | || | || | | || ||| || | | |||| || ||||| |||||||||||||||||||||||||| || |||||||| |||||||| || ||||| ||||| ||||| ||| | || || |||||||
-----------------------------------------------gtaagtgtttgaattgca-tgggattttttcgatt----tgtgaaatctttgccaatgatattctaattactgtttt--------ttgcttgtcaagCCCTGTATCATTTTTATGGATGAGATTGATGCCATTGGTGGGCGTCGTTTCAGCGAGGGAACAAGTGCTGATCGTGAAATTCAGAGAACACTCATGGAGT
upper sequence: PP1S13_419V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 6
gtactacctcttttcatctgcacttggttcagttcttccatattaaagtggttacaggagttacgcttttgttttgttgattaacctccaaaactgctaacgttgttgttgtggtggc-tactttgtggaccattatctttgcagCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTTAGCGAGGGTACTAGTGCAGATCGAGAAATCCAGCGTACCCTTATGGAGT
| ||| | | |||||| | | ||| | | | || | | | | | | || | |||| ||| |||| ||||| || ||||||||||||||||||||||| || || || ||||| || ||||| || ||||| || || ||||| || | || || |||||||
-----------------------------------------------------gtaagagcttggattttgtgaaatatgtgttccttttttataatttatgtctatccaaagttaacgttgataatgtgcttttatttttcaagCCCTGCATTATTTTTATGGATGAGATTGATGCCATCGGTGGACGCCGTTTCAGTGAGGGAACAAGTGCTGACCGTGAAATACAAAGAACACTGATGGAGTMapped 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|18335003|gb|BJ167021.1|BJ167021EST: GTTACGCCCGTGACCATCAA CCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTT
genomic: GTTACGCCCGTGACCATCAAgtactacctc ... atctttgcagCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTT
EST:
gi|37843655|gb|BJ601663.1|BJ601663EST: AAAGTGCGAGACTTATTAGGGAGATGTTTAGTTACGCCCGTGACCATCAA CCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTT
genomic: AAAGTGCGAGACTTATTAGGGAGATGTTTAGTTACGCCCGTGACCATCAAgtactacctc ... atctttgcagCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTT
EST:
gi|162188781|gb|FC364067.1|FC364067EST: GTGCGAGACTTATTAGGGAGATGTTTAGTTACGCCCGTGACCATCAA CCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTT
genomic: GTGCGAGACTTATTAGGGAGATGTTTAGTTACGCCCGTGACCATCAAgtactacctc ... atctttgcagCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTT
EST:
gi|208367874|gb|DC955337.1|DC955337EST: AAAGTGCGAGACTTATTAGGGAGATGTTTAGTTACGCCCGTGACCATCAA CCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTT
genomic: AAAGTGCGAGACTTATTAGGGAGATGTTTAGTTACGCCCGTGACCATCAAgtactacctc ... atctttgcagCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTT
EST:
gi|37853467|gb|BJ611475.1|BJ611475EST: AAAGTGCGAGACTTATTAGGGAGATGTTTAGTTACGCCCGTGACCATCAA CCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTT
genomic: AAAGTGCGAGACTTATTAGGGAGATGTTTAGTTACGCCCGTGACCATCAAgtactacctc ... atctttgcagCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTT
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:
34 (upstream exon),
17 (downstream exon)
Score:
17GTGGTTTCTAGTGCGATTGTGGATAAGTACATTGGAGAAAGTGCGAGACTTATTAGGGAGATGTTTAGTTACGCCCGTGACCATCAAgtactacctc ... atctttgcagCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTTAGCGAGGGTACTAGTGCAGATCGAGAAATCCAGCGTACCCTTATGGAGT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaactgctaacgttgttgttgtggtggctactttgtggaccattatctttgcagCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTTAGCGAGGGTACTAGTGCAGATCGAGAAATCCAGCGTACCCTTATGGAGT
tgctaac putative branch site (score: 17)
ttatcttt putative PPT
attatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactacctcttttcatctgcacttggttcagttcttccatattaaagtggttacaggagttacgcttttgttttgttgattaacctccaaaactgctaacgttgttgttgtggtggctactttgtggaccattatctttgcagCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTTAGCGAGGGTACTAGTGCAGATCGAGAAATCCAGCGTACCCTTATGGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT