Sequence
atgc intronic sequence ATGC exonic sequencegtcagtggttttcttcggtgtcatatttcagggccagaactgctagttacacacatctcagatgtttcttctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 12
gtcagtggttttcttcggtgt-catatttcagggccagaactgctag-ttacac-------acatctcagatgtt--tcttctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
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gtcagtcgcctcttttattctacttttagcatcccaagctttgcttgatttcactgtaacaaaatctcagatcttatgcttctattgcagATCCTACATACATGATACGTGCCATTCCTAGCAATGCATCTGACAATGTGTATTGCACACTGTTGGCACACAGTGTGGTTCATGGAGCCATGGCTGGATA
upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 11
-------------------------------------------------gtcagtggttttcttcggtgt-catatttcagggccagaactgctagttacacacatctcagatgtttcttctact--gcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
| | || | | ||| ||| || | | | | | || ||| || | ||| | ||| | ||||||||||||| ||||| || || | ||||||||||||||||| ||||| || |||||||| || ||||| || | || |||||||||||||| || ||
gttcgtaaagacaaaaaactatatatttatacgtatgtgtacatgtgtgcatgttcgattacatttatgtgtgcattgcatactgaaaggaggaaat--caagcattgcatttttttttactatttgacagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA
upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 11
---------------------------------------gtcagtggttttcttcggtgtcatatttcagggccagaactgctagttacacacatctcagatgtttcttctact--gcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
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gttcgttaagacaaactatacaattatacgtatgtgtgcatgtttgattatatttatgtatgcattgcatactgaaaggaggaaat--caagcattgcattt-tttttactatttgacagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA
upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 11
----------------gtcagtggttttcttcggtgtcatattt-cagggccagaactgctagttacacacatctcagatgtttcttctact--gcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
| ||| || | | || | || | | | | | | | | | | || | | |||||||||| || ||||| || || || ||||||||||||||||| ||||| || |||||||| || ||||| || | || |||||||| ||||| || ||
gtttgtaaagattaaacttcatggaattataagtgtgcacacacacactgaaaagagcaatggctgaaagagtaatgccttctctttatgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
-----------------gtcagtggttttcttcggtgtcatatttcagggccagaactgctagttacacacatctcagatgtttcttctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
|| ||| || | | || | || | || | | | || | | ||| | | | |||||||||| || ||||| || || || ||||||||||| ||||| ||||| || |||||||| || ||||| || | || |||||||| ||||| || ||
gtttgtaaagattaaaagttcatggaattatgtgtgtacacacactgaaaggagcaatggctgaaagagtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 11
gtcagtggttttcttcggtgtcatatttcagggccag--aactgctagt-tacacacatctcagatgtttcttctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
|| || || | | |||| | || | || ||| || || || | | ||| |||| ||||||| ||||| ||||| ||||| | ||||||||||| ||||| || |||||||||||||| || ||||| || | || |||||||| ||||| || ||
gtttgtatacactatctttctaatatatagaagctgggcaatggctggtctaaccaagtgctgcactttttgtctat--cagATCCTACGTATATGATCCGTGCTGTTCCAAGCAATGCATCTGACAATGTCTATTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGGTA
upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
lower sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
-------------------------------------gtcagtggttttcttcggtg-tcatatttcagggccagaactgctagttacacacat-ctcagatgt-----ttcttc------tactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
| || || | ||| | ||| | | | || |||| | || || | || | | |||||||||||||||||||||| || || | ||||||||||||||||| ||||| || ||||| |||| ||||| |||| |||||||||| ||||| || ||
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
lower sequence: PP1S282_45V6.1 (Physcomitrella patens), 3'ss of exon 12
-----------------------------------------------------------------------------------gtcagtggttttcttcggtgtcatatttcagggccagaactgctagttacacacatctcagatgtttcttctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
| | | | || | | | || | || | | || | || |||| | | |||||||||| ||||| ||||| || || || |||||||||||||| || || ||||| |||||| |||||||||| |||| ||||||| || ||||| || ||
gtacagtagccgtcaactgttctaactgttgagtgatggtgatccgtcttcctggtctacatctgtcgattttttacactgtggggaattgcttacattctggccacgtccatggtgatcttgcattcgata-agactgctcattatgccatagttctgcagATCCGACGTATATGATTCGAGCAATTCCAAGCAATGCTTCGGACAATGTCTACTGCACATTGCTGGCTCATAGCGCCATCCATGGGGCTATGGCAGGGTA
upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
lower sequence: PP1S131_40V6.1 (Physcomitrella patens), 3'ss of exon 12
---------------------------------------------------------------------------------------------------------gtcagtggttttcttcggtgtcatatttcagggccagaactgctagttacacacatctcagatgtttcttctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
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gtatgataaaatgaccaaaaccttcattggtctctctctctttctctctctttctctctctacctcacagatatcgacgtcaagtgaaaattttggactaaactagcagaagaccttgcgcttgacccagtttcaaagc----atcgagatttgactaagaataaaatcactgtggttttttagATCCTAAGTACATGATTCGAGCGATACCGAGCAATGCTTCTGACAATGTCTATTGCACCTTGCTCGCTCATGGTGCGATTCATGGAGCCATGGCTGGTTAMapped 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|5846823|gb|AI999906.1|AI999906EST: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG ATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
genomic: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
EST:
gi|6095550|gb|AW120217.1|AW120217EST: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG ATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
genomic: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
EST:
gi|76921243|gb|DV168509.1|DV168509EST: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG ATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
genomic: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
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:
46 (upstream exon),
48 (downstream exon)
Score:
273GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
273GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
Block sizes:
46 (upstream exon),
49 (downstream exon)
Score:
274GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
Block sizes:
46 (upstream exon),
49 (downstream exon)
Score:
345GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttcagggccagaactgctagttacacacatctcagatgtttcttctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
tttcttctact CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtggttttcttcggtgtcatatttcagggccagaactgctagttacacacatctcagatgtttcttctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA