Sequence
atgc intronic sequence ATGC exonic sequencegtacattgtttactttgcttcccctcttcctctcattccatacctttgtgaaccttggtttctgatacaatgtttaagtttgctcctgaataattaatgtttaattggttatgctgaacaaatactcattgttatctatcatattcaatgttaaatgcagTTGAAACTTGGGTCTCAATACTATTTCTATATGGAGACACAAACTGCACTTGCTGTTCCAGATGAAGACAATTGCATTACAGTTTACTCCTCAAACCAAT
Basic information
species | Glycine max |
transcript | GLYMA14G04950.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G04950.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 4
------gtacattgtttacttt------gcttcccctct--tcctctcattccatacctttgtga--------accttggtttctgatacaatgt-ttaagt-------ttgctcctgaataatt--aatgtttaatt---ggttatgctgaac---aaatactcattgttatctatcatattcaatgt-taaatgcagTTGAAACTTGGGTCTCAATACTATTTCTATATGGAGACACAAACTGCACTTGCTGTTCCAGATGAAGACAATTGCATTACAGTTTACTCCTCAAACCAAT
| | |||| || | ||| || | | | |||| ||| || | | | ||| || | ||| | | || |||||| | || ||| | || | | ||| | | | | | | || | || || | || ||| |||||||||| || || ||||||||||| |||||||||||||| || | ||| | || |||||||| || || || || || |||| |||| |||
gtacggacatttcgttttctcttaacacgctaaagctttaattttgctattctatatattaattagaagaacaattttgattcacactggaatctactgagcaacagagttgctctgaatgaaacgaaatatatagcctcagttcatgacaattctaggagaaataccttcaccttatttgttttttgggcacatacagGTGAAACTTGGATCCCAGTACTATTTCTACATGGAGACACAAACGGCTTTAGCTTTCCCTGATGAAGATAACTGTATAACCGTCTACTGCTCAGCGCAAA
upper sequence: GLYMA14G04950.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G27150.2 (Arabidopsis thaliana), 3'ss of exon 4
gtacattgtttactttgcttcccctcttcctctcattccatacctttgtgaaccttggtttctgatacaatgttt-aagtttgctcctgaataattaatgtttaattggttatgctgaacaaatactcattgt-tatctatcatattcaatgttaaatgcagTTGAAACTTGGGTCTCAATACTATTTCTATATGGAGACACAAACTGCACTTGCTGTTCCAGATGAAGACAATTGCATTACAGTTTACTCCTCAAACCAAT
| | | || || | | || | | | || ||| || | | |||||| | | | | | | | | | | || ||||||| || ||||| || |||| |||||||||||| ||||||| |||||||| | ||||| ||||||||||| | | || | ||| |||
---------------------------------------------------------------------gtatctcaaaactgtttccagattttcaccgccaaa---gttgtgt--agtgacatctcattttgtgtgtttgaaacttggttatttattcagTTGAGGCTAGGGTCACAGTACTTCTTCTATATGGAGCCACAAACAGCACTTGCCTTGCCAGACGAAGACAATTGTGTCAAGGTATTTAGTTCATCTCAAG
upper sequence: GLYMA14G04950.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G04580.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacattgtttactttgcttcccctcttcctctcattccatacctttgtgaaccttggtttctgatacaatgtttaagtttgctcctgaataattaatgtttaattggttatgctgaacaaatactcattgttatctatcatattcaatgttaa--------atgcagTTGAAACTTGGGTCTCAATACTATTTCTATATGGAGACACAAACTGCACTTGCTGTTCCAGATGAAGACAATTGCATTACAGTTTACTCCTCAAACCAAT
| || ||| | | | | || ||| || || || | | | || ||| | |||| ||| | || || |||| | |||||||||| ||||||||| || |||| |||||||||||||||||||| |||||||| | |||||||||||||| || | |||||| |||| |||
-------------------------------------------------------------gtattaaaat-tctctttctctctcttaatctttgata--tattaaaaaaaaataaaaaaaaatacattctta--cactatgtttgctgttgattttggttatgcagTTGAGACTTGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCACTTGCCTTGCCAGATGAAGACAACTGTTTAGTGGTTTACAGTTCAACTCAAG
upper sequence: GLYMA14G04950.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G20960.2 (Arabidopsis thaliana), 3'ss of exon 4
gtacattgtttactttgcttcccctcttcctctcattccatacctttgtgaaccttggtttctgatacaatgtttaagtttgctcctgaataattaatgtttaattggttatgctgaacaaatactcattgttatctatcatattcaatgttaaatgcagTTGAAACTTGGGTCTCAATACTATTTCTATATGGAGACACAAACTGCACTTGCTGTTCCAGATGAAGACAATTGCATTACAGTTTACTCCTCAAACCAAT
||| | | | || | | | |||| | || | | || || || || || || || | | | ||||| || |||| |||||||||||||||||||| || ||||| || || ||||||||||| || || ||||| ||| | |||
--------------------------------------------------------------------------gtggttcttttccaagacatatacacctctaaagccgtgctct----tttctaaccatcatataaaatctttgtgatt--gtgtagATAAGTTTCGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCTCTTGCAGTGCCGGATGAAGACAACTGTATGGTGGTTTATAGCTCGACTCAAA
upper sequence: GLYMA14G04950.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02410.t01 (Vitis vinifera), 3'ss of exon 4
gtacattgtttactttgcttcccctcttcctctcattccatacctttgtgaaccttggtttctgatacaatgtttaagtttgctcctgaataattaatgtttaa-ttggttatgctgaacaaatactcattgttatctatcatattcaatgttaaatgcagTTGAAACTTGGGTCTCAATACTATTTCTATATGGAGACACAAACTGCACTTGCTGTTCCAGATGAAGACAATTGCATTACAGTTTACTCCTCAAACCAAT
||| | | | || || | ||||||| ||| | | |||| |||||||||| || || | || || | | || | ||| | ||| | || ||| | | ||||||||| || || |||||||||||||||||||||||||| ||||| ||||| ||||||||||| |||||| |||||| |||| ||||
---------------------------------------gtacttct-----catttacttgttatacaattttt--ttctattcct-----attaatgtttttctttcttgttttggttttatgataaatgctttctga-------attgtcacatccagATCAGACTTGGGTCACAGTATTATTTCTATATGGAGACACAAACTGCCCTTGCAGTTCCCGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT
upper sequence: GLYMA14G04950.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02430.t01 (Vitis vinifera), 3'ss of exon 4
gtacattgtttactttgcttcccctcttcctctcattccatacctttgtgaaccttggtttctgatacaatgtttaagtttgctcctgaataattaatgtttaa-ttggttatgctgaacaaatactcattgttatctatcatattcaatgttaaatgcagTTGAAACTTGGGTCTCAATACTATTTCTATATGGAGACACAAACTGCACTTGCTGTTCCAGATGAAGACAATTGCATTACAGTTTACTCCTCAAACCAAT
||| | | | || || | ||||||| ||| | | |||| |||||||||| || | | || || | | || | ||| | ||| | || ||| | | ||||||||| || || |||||||||||||||||||||||||| ||||| |||| ||||||||||| |||||| |||||| |||| || |
---------------------------------------gtacttct-----catttacttgttatacaat-tttttttctattcct-----attaatgtttttctttcctgttttggttttatgataaatgctttctga-------attgtcacatccagATCAGACTTGGGTCACAGTATTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCGGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAGT
upper sequence: GLYMA14G04950.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02390.t01 (Vitis vinifera), 3'ss of exon 3
gtacattgtttactttgcttcccctcttcctctcattccatacctttgtgaaccttggtttctgatacaatgtttaagtttgctcctgaataattaatgtttaattggttatgctgaacaaatactcattgttatctatcatattcaatgttaaatgcagTTGAAACTTGGGTCTCAATACTATTTCTATATGGAGACACAAACTGCACTTGCTGTTCCAGATGAAGACAATTGCATTACAGTTTACTCCTCAAACCAAT
||| | | | || || | || |||| ||| || | || ||| | ||| || | | || || | | | | |||| | ||| | || ||| | ||||||||||| ||||| || |||||||||||||| |||||||| ||||| |||||||||||||| || |||||| |||||| ||| ||||
---------------------------------------gtacttct-----catttacttgttatgcaattttt---ttcctatttatattatt--tttttcctttctctttttggttttatgataaatactttctaa-------attgtcacatccagATCAAACTTGGGTCACAATATTACTTCTATATGGAGACCCAAACTGCCCTTGCAGTTCCAGATGAAGATAACTGCATTGTGGTTTACAGTGCAATACAAT
upper sequence: GLYMA14G04950.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 4
gtacattgtttactttgcttcccctcttcctctcattccatacctttgtgaaccttggtttctgatacaatgtttaagtttgctcctgaataattaatgtttaattggttatgctgaacaaatactcattgttatctatcatattcaatgttaaatgcagTTGAAACTTGGGTCTCAATACTATTTCTATATGGAGACACAAACTGCACTTGCTGTTCCAGATGAAGACAATTGCATTACAGTTTACTCCTCAAACCAAT
| | ||||| | | | || ||| || || | | | ||| || || | ||| | ||| || || || |||| || | || | || || |||| | || | | ||||||||||| || ||||||||||||||||||||||||||||| ||||| |||||||||||||||| |||||| |||||| |||| ||||
-------------------------gtatttgtcatttacttgttatacaaattttg-ttcctatttcta---ttagtgtttttctt------ttattttttggtt--ttgtgatgaataattgctga--attgtcc-tcatgtcca------------gATCAAACTTGGGTCACAGTACTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCAGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggttatgctgaacaaatactcattgttatctatcatattcaatgttaaatgcagTTGAAACTTGGGTCTCAATACTATTTCTATATGGAGACACAAACTGCACTTGCTGTTCCAGATGAAGACAATTGCATTACAGTTTACTCCTCAAACCAAT
atattcaatgttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacattgtttactttgcttcccctcttcctctcattccatacctttgtgaaccttggtttctgatacaatgtttaagtttgctcctgaataattaatgtttaattggttatgctgaacaaatactcattgttatctatcatattcaatgttaaatgcagTTGAAACTTGGGTCTCAATACTATTTCTATATGGAGACACAAACTGCACTTGCTGTTCCAGATGAAGACAATTGCATTACAGTTTACTCCTCAAACCAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC