Sequence
atgc intronic sequence ATGC exonic sequence...tgtgcgctttgaatttgctgtctgtttttatctctggtatgtgaaacaattacaacacctgacaagtatttgtctcattttcatctttcgcgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G000923_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G13850.1 (Arabidopsis thaliana), 3'ss of exon 2
tgtgcgctttgaatttgctgtctgtttt--tatctctggtatgtgaaaca-attacaacacctgacaag-tat-ttgtctcattttcatctttcgc--------gacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT
| | | |||| | || ||| || | | | ||| | || || | |||| || || | | || | | || | |||| || ||||| ||| ||||| ||||||||||||||| |||||||| ||||| || || || ||| |||||||||| ||||| || |||||||||||
----tggtgaaagtttgatacttggtttggtaaatatagaatgaggaattcggtatcatttctgatgagctacgtcatgacagtgctgtgatttgtttaaccagGACATGATGGGGAGGCCGGTGGCCGGTCAAAGCAAAGCAGAAGTGAGAAAAAGAGTCGTAAAGCTATGTTGAAGCTTGGGATGAAACCAATCACTGGTGT---------
upper sequence: GRMZM2G000923_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 2
------tgtgcgctttgaatttgctgtctgtttttatctctggtatgtgaaac--aattacaacacctgacaagtatttgtctcattttcatcttt---cgcgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT
| ||||| || || | |||| || || | |||| ||| ||| | || || | |||| | | || | ||| ||| || || || | || |||||||| |||||||| |||||||||||||| ||||| |||||||| |||||||||||||| ||||||||||||||
ttttcaaataatctttgcgttgact-tgtgttgatagacatg-tttgtggaacttaatgttatcatctattttattcttgttgattggtgattggaaaacagGACTAGATGGAGAGGCAGGAGGTAAGTCAAAACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGT---------
upper sequence: GRMZM2G000923_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 2
--tgtgcgctttgaatttg---ctgtctgttt-ttatctctggtatgtgaaacaattacaacac--ctgacaagtatttgtctcattttcatctttcgcg-----acaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT
| | ||| | | |||| || | | ||| | || || ||| | || || | | | | | ||| | | || || ||| | ||| ||||| ||||| | ||||||||| ||| | ||||| ||||||||||||||||| ||| |||||||||| ||||| ||||| | ||
gaattatgttttaaggaggaaactgtgtgctgaccaaaactgcttggttgttcatttaaatcatggcttatta-tgccagctttattcttgtgttaagcagGAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAAAGAAGAGCCGCAAGGCAATGTTGAAGCTTGGAATGAAACCCATTCCAGG------------
upper sequence: GRMZM2G000923_T02 (Zea mays), 3'ss of exon 2
lower sequence: EDO97954 (Chlamydomonas reinhardtii), 3'ss of exon 1
---------tgtgcgctttgaatttgctgtctgtttttatctctggtat-gtgaaacaattacaacacctgaca-agtatttgtctcattttcatctttcgcgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT
||||| | | | | | | | || | || | || | | | | ||| | ||| | || || | | || | || || | |||| ||||| ||| | || ||||||||||||||||||||||||| |||||| |||||||||||| ||||||| || |
gctcagcgtctggcgctgtcggctgggcgagcgatgccagctttagtttcgtcggcccacagggatgctgaacatggcgcatgtgtgatgttggctgc-----agATGAGGAGGGTGGCGCTGGCCGCGGCAAGCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGAC------
upper sequence: GRMZM2G000923_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S122_100V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------tgtgcgctttgaatttgctgtctgtttttatctctggtatgtgaaacaattacaacacctgacaagtatttgtctcat------tttcatctttcgc-gacaagaagGGGATGCCAGT-GGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT
| | | |||||| | | | | | | | |||| | | || | | ||||| ||| | | | || | | | | || || | | || ||||||||||| ||| | |||||||||||||| | |||||||||| |||||||||||||| || || | || ||
gtgaagaagcccattctaactcccatcacttgctgcgttcagtgaatttcaatcaacaagataattttcattttatataa-tctccaactcatgtgaagtttgaacatctgcagGCGAAGACGGTCTGACTGCAGGTAAGTCAAAGCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAACCAGTCCCCGGCGT---------
upper sequence: GRMZM2G000923_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------tgtgcgctttgaatttgc---tgtctgtttttatctctggtatgtgaaacaattacaacacctga-caagtatttgtctcattttcatctttcgcgacaagaagG---GGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT
| | | ||||| | || ||| || || | | | ||||| ||| | ||| | | | || | |||| | | |||| || | ||| |||| ||||| ||||| ||| | |||||||||| ||| | |||||||||| |||||||||||||||||| | || |
gtctgttgtcaacgacccttgccaacgtctattgacccaagcctctgttcagaattagtgagtgatgctttctaaaattgtaagctagaggcattactctgtttgatcgagtttctaaatt-ttcttttcttgcagGTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGAAGAAAAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACCGA------------
upper sequence: GRMZM2G000923_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S539_1V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------tgtgcgctttgaatttgctgtctg--tttttatctctggtatgtgaaacaatt-acaacacctgacaagta-tttgtctcattttcatct----ttcgc-gacaagaagGG----GATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT
|| ||| |||| || | | | | | | || | ||| | | ||| | | | ||| | ||| ||| | ||||| | | | | | ||| |||| ||||| ||||| ||| | |||||||||||||| | |||||||||| |||||||||||||||||| | ||||
gtcctttccatcaaatccccttcccatacttttcgtaactcttgcctttgttgacaagactgtgagtaattcttagttagacatctcgtctttcttgatagggaatttcacgtgtttacatatgtacttcgcagGTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACTGA------------
upper sequence: GRMZM2G000923_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 2
tgtgcgctttgaatttgctgtctgtttttatctctggtatgtgaaacaattacaacacctgacaagtatttgtctcattttcatctttcgcgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT--
|| | | || || |||| | || | ||||| | || || || ||||||||| |||| |||||||||||||| ||||| |||| |||||| || ||||||||| | ||||| || | | ||
-------------------------------------------------------------------gttcctactttctttatgtttctt--ccaggcgagGATGGAACGGGGAAATCGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGAMapped 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|24766680|gb|CA401827.1|CA401827EST: GGATGATGATGAACTCGATG GGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCA
genomic: GGATGATGATGAACTCGATGgtgagttatt ... cgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCA
EST:
gi|166559422|gb|EG319037.1|EG319037EST: GAAGATGAGGACGATGACGATGATGACAAGGATGAATGATGAACTCGATG GGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGA
genomic: GAAGATGAGGACGATGACGATGATGACAAGGATG-ATGATGAACTCGATGgtgagttatt ... cgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGA
EST:
gi|78025838|gb|DV494225.1|DV494225EST: ATGACAAGGATGATGATGAACTCGATGAAG
genomic: ATGACAAGGATGATGATGAACTCGAT---Ggtgagttatt ... cgacaaga
EST:
gi|60396469|gb|DN229338.1|DN229338EST: CGATGACGATGATGACAAGGATGATGATGAACTCGATG GGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCA
genomic: CGATGACGATGATGACAAGGATGATGATGAACTCGATGgtgagttatt ... cgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCA
EST:
gi|60348322|gb|DN215295.1|DN215295EST: GACAAGGATGATGATGAACTCGATG GGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCA
genomic: GACAAGGATGATGATGAACTCGATGgtgagttatt ... cgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCA
EST:
gi|60352329|gb|DN219302.1|DN219302EST: CGATGACGATGATGACAAGGATGATGATGAACTCGATGAAG
genomic: CGATGACGATGATGACAAGGATGATGATGAACTCGAT---Ggtgagttatt ... cgacaaga
EST:
gi|78025744|gb|DV494131.1|DV494131EST: ATGACGATGATGACAAGGATGATGATGAACTCGATG GGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCA
genomic: ATGACGATGATGACAAGGATGATGATGAACTCGATGgtgagttatt ... cgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCA
EST:
gi|31910389|gb|CD651399.1|CD651399EST: GATGACAAGGATGATGATGAACTCGATG GGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCA
genomic: GATGACAAGGATGATGATGAACTCGATGgtgagttatt ... cgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCA
EST:
gi|120480064|gb|EH210716.1|EH210716EST: ATGACAAGGATGATGATGAACTCGATG GGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCA
genomic: ATGACAAGGATGATGATGAACTCGATGgtgagttatt ... cgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCA
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 4 RNA-Seq libraries.
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
1089GCAGAGGAAGTTGTGGTGGAGGATGAGGAGGAGGAAGATGAGGACGATGACGATGATGACAAGGATGATGATGAACTCGATGgtgagttatt ... cgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
1321GCAGAGGAAGTTGTGGTGGAGGATGAGGAGGAGGAAGATGAGGACGATGACGATGATGACAAGGATGATGATGAACTCGATGgtgagttatt ... cgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
1298GCAGAGGAAGTTGTGGTGGAGGATGAGGAGGAGGAAGATGAGGACGATGACGATGATGACAAGGATGATGATGAACTCGATGgtgagttatt ... cgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
770GCAGAGGAAGTTGTGGTGGAGGATGAGGAGGAGGAAGATGAGGACGATGACGATGATGACAAGGATGATGATGAACTCGATGgtgagttatt ... cgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaattacaacacctgacaagtatttgtctcattttcatctttcgcgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT
acctgac putative branch site (score: 770)
ttttcatctttcgc putative PPT
aagtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgcgctttgaatttgctgtctgtttttatctctggtatgtgaaacaattacaacacctgacaagtatttgtctcattttcatctttcgcgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - -tgctgtc
- - - - - - - - - - - tgttttt
- - - - - - - - - - - - - - - - - - gtatgtg
- - - - - - - - - - - - - - - - - - - - - -aaacaat
- - - - - - - - - - - - - - - - - - - - - - - - - - caacacc