Sequence
atgc intronic sequence ATGC exonic sequencegtatgagaattctcctatgattgtgtttcttggattttttaagtattattggaaaaaataattgacattaatgaagtgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
gtatgagaattctcctatgattgtgtttcttgga-----ttttttaagtattattggaaaaaataattgacattaatgaagtgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC
|| ||| | |||| || || || || || | |||| | || | ||| | ||| | ||| || ||||||||||||| || ||||||||||| ||||| ||||||||||| || ||||| ||||||||||||| |||||||| ||||| |||||| ||||| ||||||
gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
upper sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G17250.1 (Glycine max), 3'ss of exon 4
gtatgagaattc-tcctatgattgtgtttcttggattttttaagtattattggaaaaaataattga--cattaatgaagt----gcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC
|||||| ||| | | || || | | || | | | || | || | ||| | || |||||||||||||| |||||||||||| |||| || ||||| ||||| |||||| | |||||||| |||||||| || || ||| | | || |
gtatgactcttcgttttgctcttctgctcatccatgttacctacagaaaataatgcaattggttaaaccatgccttttgtttaaacagGGTGAGAAAGAGTGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCTGCTGGCACATCATTGCCAA
upper sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G02550.1 (Glycine max), 3'ss of exon 4
gtatgagaattctcct-atgattgtgtttcttggattttttaagtattattggaaaaaataattga--cattaatgaagt----gcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC
|| ||| |||| | || || | || || | | | | ||| ||| | ||| | || ||||||||||||||||||||||||||| | || || ||||| ||||| |||||| | |||||||| |||||||| || || ||| | | || |
gtttgactcttctttttgctcttctgctcgttcatgttacctacaccaaataaatgtaatgattaaaccatgccttttgtttaaacagGGTGAGAAAGAATGCTCCTACTATTTAAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCTGCTGGCACATCATTGCCAA
upper sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G28820.1 (Glycine max), 3'ss of exon 4
-------------------------------gtatgagaattctcctatg-attgtgtttc----ttggattttttaagtattattggaaaaaat--aattgacattaatgaagtg-cagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC
| | | || || | || ||||| | ||| | || |||| | | | ||| || ||| | ||||||||||| || || ||||| ||| |||| || || ||||||||||||||| | || |||||||| |||||||||| || ||| || | | | |
gtctgtatcactttttgtatttactacataaggctaggcatgcttttgaatgttctgttttgttttctgatcatggaaatattttgatccgagtttgaatgtttataaatatgataacagGGTGAGAAGGAGTGTTCCTATTATGTGAAAACAGGACAATGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCAGTTCCTGCTGGCATCCAAATTCCAC
upper sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G37980.1 (Glycine max), 3'ss of exon 4
----------------------------------------gtatgagaattctcctatgattgtgtttcttg-gattttttaagtattattggaaaaaataattgacattaatgaagtgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC
| || ||||| | | | | | | || || ||| | |||| || || ||| |||| | | |||| |||||| ||||||| || ||||| || |||| ||||| || |||||||||||| | || |||||||| ||||||||| | || || | | ||
gtctgtatcagtttgtgtttactgcgtaaaattatgtgtgctttgtgaattttggtgtcactcttttcctaacgatgatggaagttttgttc-aaacttgaattttcgtgcatgata-acagGGTCAGAAAGAGTGTTCCTATTACGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCACAGCCTGCAGGCGTCCAAGTTCTAG
upper sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G02720.2 (Glycine max), 3'ss of exon 3
----------------------------------------gtatgagaattctcctatgattgtgtttctt-ggattttttaagtattattggaaaaaataattgacattaatgaagtgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC
| || |||| | | | | | | || || |||| | |||| || || || |||| | | |||| |||| ||||||||| || ||||| ||| |||| ||||| || |||||||||||| | || |||||||| || |||||| | || || | | |
gtctgtatcagtttgtgtttattgcgtaaaattatgcgtgctttgggaatgttggtgtcactcttttcctaaggatgatggaagttttgttctaacttg-aattttcgtgcatgata-acagGCTGAGAAAGAGTGTTCCTATTATGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCACCATCCACAGCCTGCAGGCGTCCAAGCTCTAG
upper sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G10230.1 (Glycine max), 3'ss of exon 4
----------------------------------------------gtatgagaattctcctatgattg-tgtttcttggattttttaagtattattggaaaaaataattgacattaatgaagtgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC
| ||| ||| | || || || | | | ||| | | | | || | || | |||||| ||||||||||| || || ||||| ||| |||| || || ||||||||||||||| | || |||||||| |||||||||| || ||| | | | |
gtctgtgtcacttttttgaatttacttacataaggctaagagtgttttgtgaatgttcagttttgttttctgacagtggaaagattttgatctgaatttgaatgtttataaatgataatgata-acagGGTGAGAAGGAGTGTTCCTATTATGTGAAAACAGGACAATGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCAGTTCCTGCTGGCGTCCAAATTCCAG
upper sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G02540.1 (Glycine max), 3'ss of exon 4
gtatgagaattctcctatgattgtgtttcttggattttttaagtattattggaaaaaataattgacattaatgaa------------gtgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC
|||||| ||| || | || || | | | | ||| | ||| || || |||| | |||| |||||||||||||||||||||| |||| || ||||| ||||| | |||| | |||||||| |||||||| || | || | | || |
gtatgataatggcact-tctttttgctcttcttctccctcgcgtaattgacagcaaattatgcgatgttaagccatgccttttgtttaaacagGATGAGAAAGAATGCTCCTACTATTTGAAAACAGGGCAGTGCAAATATGGTATATCTTGTAAATTCCATCATCCTCAACCGGCGGGCACATCATTGCCAG
upper sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G17260.2 (Glycine max), 3'ss of exon 4
gtatgagaatt-ctcctatgattgtgtttcttggattt--tttaagtattattggaaaaaataatt----gacattaatgaagt----gcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC
|||||| ||| | | | | ||| ||||| | | ||| | | | | ||| |||| | || ||||||||||||||||||||||||||| |||| || ||||| ||||| |||||| | |||||||| |||||||| || | ||| | | || |
gtatgataatgacacttcttgttgctcttcttctgcctcgtgtaattgacagcaaatgatgcaatgttaaaacatgccttttgtttaaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCGGCTGGCACATCATTGCCAG
upper sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT2G47850.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgagaattctcctatgattgtgtttcttggattttttaagtattattggaaaaaataattgacattaatgaagtgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC
| || || | | ||| | | | | || | | | || || || || ||||||| || ||||||||||||||| |||| || ||||||||||| |||||| || ||||||||||||||||| | || ||||| | | || | |
--gtaagc-tttgtttccactcatgtcaaataaaaggctagtctcgagtttgcatgatctttt---ataaactctttgtagGGTGATAACGAATGCTCCTACTATTTGAAAACGGGGCAATGCAAATTTGGTATAACCTGTAAATTTCATCATCCTCAGCCTGCTGGTACTACTGTCCCAC
upper sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatgagaattctcctatgattgtgtttcttggattttttaagtattattggaaaaaataattgacattaatgaagtgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC------------------------------------------------------------------------------
| || || | | ||| | | | | || | | | || || || || ||||||| || ||||||||||||||| |||| || ||||||||||| |||||| || ||||||||||||||||| | || ||||| | | || | |
--gtaagc-tttgtttccactcatgtcaaataaaaggctagtctcgagtttgcatgatctttt---ataaactctttgtagggtgataacgaatgctcctactatttgaaaacggggcaatgcaaatttggtataacctgtaaatttcatcatcctcagCCTGCTGGTACTACTGTCCCACCACCACCAGCATCTGCACCTCAGTTTTATCCATCGGTGCAGTCACTTATGCCTGACCAGTATGGAGGTCCATCTTCTA
upper sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv07s0104g01460.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------gtatgagaattctcctatgattgtgtttct----tggattttttaagtattattggaaaaaataattgacattaatgaagtgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC
|| | | | ||| |||| || |||| || | | || | ||||| | | || | ||||||||||||||||||||||||||| |||| || ||||| |||||||||||| ||||||||||| |||||||| || | ||| | | || |
gttgggatttggtttattcttcaccttttctaatcaaattcgttttactaaatcagcatggttgtaatttgggaatggacacttccatttagcttatgtttatgaattggaaattttgcaa--cagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAGTTTGGTATAACATGTAAATTCCATCATCCTCAACCAGCTGGCACATCATTGCCAG
upper sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv05s0020g01650.t01 (Vitis vinifera), 3'ss of exon 4
-------------------gtatgagaattctcctatgattgt---gtttcttggattttttaagtatta---ttggaa--aaaataattgaca--ttaatgaagtgc---agGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC
| | | | |||| | | ||| ||| ||||| | || | | ||| | || | | | | || || ||| ||||||| ||||| |||||||||||| ||||||| || | |||||||||||| ||||||||||| ||||||||| | | | | || | || |
gtctgtgtttgttgcaactttttttaatctatcctgttaatgttagatttattggaatcacatagcctgaagtttgcagttaagttggctcaaagcttgatatgttgctacagGGTGAAAAAGAGTGCTCCTACTATGTGAAGACAGGACTTTGCAAGTTTGGTGAAACATGTAAATTCCATCATCCACAGCCAGATAGCATACAACTGTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttggattttttaagtattattggaaaaaataattgacattaatgaagtgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC
cattaat putative branch site (score: 3)
attttttaagtattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgagaattctcctatgattgtgtttcttggattttttaagtattattggaaaaaataattgacattaatgaagtgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG