Sequence
atgc intronic sequence ATGC exonic sequence...tataaggtgtccttaacccaaaggtgagactcagcgcccgccacatgaatttactctgcgcatgaaactattctaaactgaatcaattcatgcttctcagGTTGTTCCAGCCTGGCTTAACTGCTTGCCAATAAAAGATGACAAGATTGAAGCTAAAGCTGTACATGAACAACTTTGCTCAATGGTGGAGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G011246_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g38760.1 (Oryza sativa), 3'ss of exon 17
tataaggtgtccttaacccaaaggtgagactcagcgcccgcca---catgaattt-----actctgcgcatgaaactattctaaactgaatcaattcatgcttctcagGTTGTTCCAGCCTGGCTTAACTGCTTGCCAATAAAAGATGACAAGATTGAAGCTAAAGCTGTACATGAACAACTTTGCTCAATGGTGGAGAG
| ||| | || | ||||| |||| | ||| ||| | | | | | ||| || | | ||| ||||||||| | |||| |||| ||||||||| |||||||| ||||||||||||||||||||||| |||| |||||| || || || | ||||||||| || ||
-------tagatttagtctgaaccttgttttcagctcccgtaagaccatatattgctaaaaagatacatgttgtattatcctcatcc-aatgtattcatgctctttagGTCATTCCTGCCTGGCTTGGTTGCTTGCCTATAAAAGATGACAAGATTGAAGCAAAAGTTGTACACGATCAGCTCTCCTCAATGGTTGAAAG
upper sequence: GRMZM2G011246_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G28950.1 (Glycine max), 3'ss of exon 19
---------------------------------------------tataaggtgtccttaacccaaaggtga--gactcagcgcccgccacatgaatttactctgcgcatgaaactattctaaac-----tgaatcaat---tcatgcttctcagGTTGTTCCAGCCTGGCTTAACTGCTTGCCAATAAAAGATGACAAGATTGAAGCTAAAGCTGTACATGAACAACTTTGCTCAATGGTGGAGAG
| | | | || | | ||| | || | | || || | | | ||| | || | || || | | ||||| || ||||| ||||| || ||||| ||||| ||||||||||||| ||| |||||| || |||| ||| ||||| |||||||| ||||||| |||||
gtcagtacatattttccgtttataacttgcctttgtggttttggttcttgattatgtttgtcattattatgatcaattctttctgagtctgatttgttgtttttaggt-tgagatgatggttaatatttttgtaatgttctgtcatgtttg-cagGTAGTTCCTGCATGGCTAAACTGTTTGCCAATAAAAGGTGATTTGATTGAGGCCAAAGTTGTGCATGATCAACTTTGTTCAATGGCTGAGAG
upper sequence: GRMZM2G011246_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G29010.1 (Glycine max), 3'ss of exon 17
tataaggtgtccttaacccaaaggtgagactcagcgcccgccacatgaatttactctgcgcatgaaacta--ttctaaactgaatca--attcatgcttctcagGTTGTTCCAGCCTGGCTTAACTGCTTGCCAATAAAAGATGACAAGATTGAAGCTAAAGCTGTACATGAACAACTTTGCTCAATGGTGGAGAG
| | | | |||| | || | | | | | | || | |||||| || | |||||| | ||||| ||| | | |||||||||||| |||||||| | |||||||| ||||||| ||| ||||||||||| | ||| ||||| |||||||| |||||||| || ||
gacactgattttttaaatcctta-tggaaatgaaagttt---agagaaaaatcctctgcctgtgtttttgatttctaacttcaatcattattgcttgatatcagGTTGTTCCTGCCTGGCTAAGTTGCTTGCCTATAAAAGGTGATTTAATTGAAGCTAAGGTTGTGCATGACCAACTTTGTTCAATGGTTGAAAG
upper sequence: GRMZM2G011246_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G04400.1 (Glycine max), 3'ss of exon 17
tataaggtgtccttaacccaaaggtgagactcagcgcccgccacatgaatttactctgcgcatgaaactattctaaactgaatcaattcatgcttc---tcagGTTGTTCCAGCCTGGCTTAACTGCTTGCCAATAAAAGATGACAAGATTGAAGCTAAAGCTGTACATGAACAACTTTGCTCAATGGTGGAGAG
| | || || | ||| | | | || | | ||| || | || ||||| | || ||| ||||| |||||||||||| |||||||| || |||||||| ||||||| ||| |||||||| || | ||| ||||| |||||||| |||||||| || ||
--tgacacttcttttaaatccttatgaaaatgaacgtttag-agaaaaatcccctgcctgtgtgtttgatatctaacttcaagttattattgcttgaaatcagGTTGTTCCTGCCTGGCTAAATTGCTTGCCTATAAAAGGTGATTTAATTGAAGCCAAGGTTGTGCATGACCAACTTTGTTCAATGGTTGAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaatttactctgcgcatgaaactattctaaactgaatcaattcatgcttctcagGTTGTTCCAGCCTGGCTTAACTGCTTGCCAATAAAAGATGACAAGATTGAAGCTAAAGCTGTACATGAACAACTTTGCTCAATGGTGGAGAG
ttctaaa putative branch site (score: 2)
tgcttctc putative PPT
tattctaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tataaggtgtccttaacccaaaggtgagactcagcgcccgccacatgaatttactctgcgcatgaaactattctaaactgaatcaattcatgcttctcagGTTGTTCCAGCCTGGCTTAACTGCTTGCCAATAAAAGATGACAAGATTGAAGCTAAAGCTGTACATGAACAACTTTGCTCAATGGTGGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - aacccaa
- - - - - - - - - - - - - - - - - - -ccgccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaatc