Sequence
atgc intronic sequence ATGC exonic sequencegtaagatcctttcctaggtggttacagtattttttttatttctttataaatcatggttggctgttataagttgataacacatcttttgtcagtttgtctgaagaattaaataaaattgatgtcaaaaagctgtattttttcagtaattattgtgcctaacatatgttcttgcatgtaatgaatgaattctgcagATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G031107_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g38840.1 (Oryza sativa), 3'ss of exon 7
gtaagatcctttcctaggtggttacagtattttttttatttctttataaatcatggttggctgttataagttgataacacatcttttgtcagtttgtctgaagaattaaataaaattgatgtcaaaaagctgtat--tttttcagtaattattgtgcctaacatatgttcttgcatgtaatgaatgaattctgcagATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG
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gtaatatgcttttctatgtagtc------ctttgtatttttatttgtcaactgtagttacat-ctatga----------catcctctgtta-ttggtataaag--ttgaatggattagttttggaaattctggaaagttttatcattatcatggtgcgaacaacatgtgcttgaacataataaatatatgctgcagATTGTATTCAGAGAGGACTTTGGGACTGAAGGACGTGGAGGGTACTTTGATCAATATGG
upper sequence: GRMZM2G031107_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 7
gtaagatcctttcctaggtggttacagtattttttttatttctttataaatcatggttggctgttataagttgataacacatcttttgtcagtttgtctgaagaattaaataaaat-tgatgtcaaaaagctgtattttttcagtaattattgtgcctaacatatgttcttgcatgtaatgaatgaat-tctg-cagATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG
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-------------------------------------------------------------------------------------------------cttaacaatattttgttgccttatctaattcaactactgcattaccgtatttgatatggcacacttttaaacttgagttttgctgtcaattctctgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAATATGG
upper sequence: GRMZM2G031107_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagatcctttcctaggtggttacagtattttttttatttctttataaatcatggttggctgttataagttgataacacatcttttgtcagtttgtctgaagaattaaataaaattgatgtcaaaaagctgtattttttcagtaattattgtgcctaacatatgttcttgcatgtaatgaatgaattctgcagATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG
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--------------------------------------------------------------------------------------------------gtgagagctgcata--gctaagacagaaatagtcagactgtttgttatttagagt---caattcacattttcaaatgcttt-------tcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
upper sequence: GRMZM2G031107_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 7
gtaagatcctttcctaggtggttacagtattttttttatttctttataaatcatggttggctgttataagttgataacacatcttttgtcagtttgtctgaagaattaaataaaattgatgtcaaaaagctgtattttttcag-taattattgtgcctaacatatgttcttgcatgtaatgaatgaattct---gcagATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG
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-------------------------------------------------------------------------------------------ggttacctcaaaatgt---tgaagtc----tctgatcgttttctatttcaaaataagtaatatgccataaacttaagcatgtggctattattttttttctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG
upper sequence: GRMZM2G031107_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S73_244V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaagatcctttcctaggtggttacagtattttttttatttctttataaatcatggttggctgttataagttgataacacatcttttgtcagtttgtctgaagaattaaataaaattgatgtcaaaaagctgtattttttcagtaattattgtgcctaacatatgttcttgc-atgtaatgaatgaattctgcagATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG
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-----------------------------------------------------------------------------------------------gttaaaatagatcaatgcagtctatacatctctatttcatagtttgagaaggtgttcggatgtggttaccctctgattattttctagtttcatcttgcagATTGTTTTCAAGGAGGACTTTGGAACTGAAGGACGAGGCGGCTACTTCGACGAATACGG
upper sequence: GRMZM2G031107_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S222_130V6.2 (Physcomitrella patens), 3'ss of exon 7
gtaagatcctttcctaggtggttacagtattttttttatttctttataaatcatggttggctgttataagttgataacacatcttttgtcagtttgtctgaagaattaaataaaattgatgtcaaaaagctgtattttttcagtaattattgtgcctaacatatgttcttgcatgtaatgaatgaattctgcagATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG
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---------------------------------------------------------------------------gagctagcatttatcaatatgtcttcg--atta--caccatttatttctga--------tcacttcagaaaa----gtagctgttctctga---tgagtttgttagttacatctcgcagATTGTTTTTAAGGAGGACTTTGGAACTCAAGGACGAGGTGGTTATTTTGATGAGTATGG
upper sequence: GRMZM2G031107_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S192_39V6.5 (Physcomitrella patens), 3'ss of exon 6
gtaagatcctttcctaggtggttacagtattttttttatttctttataaatcatggttggctgttataagttgataacacatcttttgtcagtttgtctgaagaattaaataaaattgatgtcaaaaagctgtattttttcagtaattattgtgcctaacatatgttct----tgcatgtaatgaatgaattctgcagATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG
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--------------------------------------------------------------------------------------------catgtctacagttcttaattactttattgtttcca------ctttggttataaattgatgtgaaaagaggttgctccctaatgcttttgttggctacttctggcagATCGTTTTCAAGGAGGACTTTGGAACTCAAGGACGGGGTGGTTACTTCGACGAATATGGMapped 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|111146774|gb|EE258268.1|EE258268EST: ACCGCTTATTTTTGCCTCTCTGGAACCGTGATAACATAGCTAACGTACAG ATCGTATTTAAGGAAGACTTTGGAACTGAAGGACGTGGAGGATATTTTGAT
genomic: ACCGCTTATTTTTGCCTCTCTGGAACCGTGATAACATAGCTAACGTACAGgtaagatcct ... aattctgcagATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGAT
EST:
gi|60672339|gb|DN475101.1|DN475101EST: ACCGCTTATTTTTGCCTCTCTGGAACCGTGATAACATAGCTAACGTACAG ATCGTATTTAAGGAAGACTTTGGAACTGAAGGACGTGGAGGATATTTTGAT
genomic: ACCGCTTATTTTTGCCTCTCTGGAACCGTGATAACATAGCTAACGTACAGgtaagatcct ... aattctgcagATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGAT
EST:
gi|18661166|gb|BM501251.1|BM501251EST: CATAGCTAACGTACAG ATCGTATTTNAGGNGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGAT
genomic: CATAGCTAACGTACAGgtaagatcct ... aattctgcagATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagtaattattgtgcctaacatatgttcttgcatgtaatgaatgaattctgcagATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG
gcctaac putative branch site (score: 2)
aattattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatcctttcctaggtggttacagtattttttttatttctttataaatcatggttggctgttataagttgataacacatcttttgtcagtttgtctgaagaattaaataaaattgatgtcaaaaagctgtattttttcagtaattattgtgcctaacatatgttcttgcatgtaatgaatgaattctgcagATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT