Sequence
atgc intronic sequence ATGC exonic sequencegtttgttttgatcagatatgaatatttatattaactttgaacgttgatatgttaatatttgttgcaactgatgcacatgatttcccatgggcagGATATGGTTGCTTTCTCTTGTTGTGTTTTCGATGGTGGAAAACAGGAGAGAGAAGACATGATTGCAGCTAGAGAAAGAGGTTGGAAAGGGAAATTTACAA
Basic information
species | Glycine max |
transcript | GLYMA20G02130.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G02130.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g62390.1 (Oryza sativa), 3'ss of exon 3
------gtttgttttgatcagatat-------gaatatttatattaactttgaacgttgat----------atgttaata------------tttgttgc-----------aactgatg--cacatgatttcccatgggcagGATATGGTTGCTTTCTCTTGTTGTGTTTTCGATGGTGGAAAACAGGAGAGAGAAGACATGATTGCAGCTAGAGAAAGAGGTTGGAAAGGGAAATTTACAA
||| || || | | | || || |||| || || ||||| | |||| || |||| |||| | || || || |||||| | | ||||||||||||||| |||||||||||||| ||||| || || || |||||| | || || |||||| || || || ||||||| ||| || ||||| |
gttagtctttcttctgttaacaaatcgttctggactattcatgatacctttgggtgctgattctgtccaaaataataatggggtccgaatcccctgtttctcagacaagagaattgtcaaccaattgatttttcttttgcagGATATGGTTGCATTCTCTTGTTGTGTCTTCGACGGGGGTGAAAAGGAGAAGAAGGAACTGGATGCAGCCAGGGAGAGGGGTTGGAGAGGAAAGTTTACTA
upper sequence: GLYMA20G02130.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G094771_T01 (Zea mays), 3'ss of exon 6
-------------------------------------------------gtttgttttgatcagatatgaata--tttatattaactttgaacgt----tgatatgttaatatttgttgcaactgatgcacatgatt---------tcccatgggcagGATATGGTTGCTTTCTCTTGTTGTGTTTTCGATGGTGGAAAACAGGAGAGAGAAGACATGATTGCAGCTAGAGAAAGAGGTTGGAAAGGGAAATTTACAA
|| | | || | | || ||| | || ||| || || ||||| || | | | || || | | | || | ||||||||||| || |||||||||||||| || |||||||| | | |||| | || || ||||||||| |||| |||||||| ||||||||||||||
gttggttttctatccccatttgttcctgaaacaattaaatattccaagggtgtacaggaaacacccaagtttacttttctgttcgtttttgttgtctgatggtatgtccatggtgagtagactggagaattatcaatcactaaccattcctttttcagGATATGGTAGCCTTCTCTTGTTGTGTCTTTGATGGTGGTGACAATGAGAAGAAGGAACTGGATGCAGCTAGGGAAAAAGGTTGGAGAGGGAAATTTACAA
upper sequence: GLYMA20G02130.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G094771_T01 (Zea mays), 3'ss of exon 6
-------------------------------------------------gtttgttttgatcagatatgaata--tttatattaactttgaacgt----tgatatgttaatatttgttgcaactgatgcacatgatt---------tcccatgggcagGATATGGTTGCTTTCTCTTGTTGTGTTTTCGATGGTGGAAAACAGGAGAGAGAAGACATGATTGCAGCTAGAGAAAGAGGTTGGAAAGGGAAATTTACAA
|| | | || | | || ||| | || ||| || || ||||| || | | | || || | | | || | ||||||||||| || |||||||||||||| || |||||||| | | |||| | || || ||||||||| |||| |||||||| ||||||||||||||
gttggttttctatccccatttgttcctgaaacaattaaatattccaagggtgtacaggaaacacccaagtttacttttctgttcgtttttgttgtctgatggtatgtccatggtgagtagactggagaattatcaatcactaaccattcctttttcagGATATGGTAGCCTTCTCTTGTTGTGTCTTTGATGGTGGTGACAATGAGAAGAAGGAACTGGATGCAGCTAGGGAAAAAGGTTGGAGAGGGAAATTTACAA
upper sequence: GLYMA20G02130.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G14970.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------gtttgttttgatcagatatgaat-atttatattaactttgaacgttgatatgttaatatt-tgttgcaactgatgcac-atgatttcccatgggcagGATATGGTTGCTTTCTCTTGTTGTGTTTTCGATGGTGGAAAACAGGAGAGAGAAGACATGATTGCAGCTAGAGAAAGAGGTTGGAAAGGGAAATTTACAA
| | ||| | | || || | | | | |||| ||| ||| || || | | || ||| || | | | | |||||||||||||| |||||||||||||| || ||||||||| | || || | | ||||||||||||| ||||||||| |||| ||||||||||| || ||||
gtttgtaacctgtaaagaagaaacgcatcaggaatctttcacttgtccctttatcatggctgattattctgaaaacagatctgtatctaaggtgagagatataatacactataagaacatgttg-cagGATATGGTTGCGTTCTCTTGTTGTGTATTTGATGGTGGAGACCAAGAAAAACAAGACATGATTGCCGCTAGAGAACGAGGATGGAAAGGGAAGTTCACAA
upper sequence: GLYMA20G02130.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0011g05000.t01 (Vitis vinifera), 3'ss of exon 6
gtttgttttgatcagatatgaatatttatatta------actttgaacgttga------------tatgttaatatttgttgcaactgatgca-catgatttcccatgg-gcagGATATGGTTGCTTTCTCTTGTTGTGTTTTCGATGGTGGAAAACAGGAGAGAGAAGACATGATTGCAGCTAGAGAAAGAGGTTGGAAAGGGAAATTTACAA
||||||||| ||||| || || | | | ||||||| || || ||| | ||| || || || || |||| ||| ||| | ||||||||||||||||||||||||||||| || ||||||||| | | || | | ||||||||| |||||| || ||||||||||||| || || |||||||
gtttgttttactcagaagtgtttagctttcctctttgttactttgagcgccgaaaatggaatccttatctcaatcttggtagcttttg-tgcatcatatcttctctcattacagGATATGGTTGCTTTCTCTTGTTGTGTATTTGATGGTGGAGAGGAAGAAATACAAGACATGAATGCAGCAAGGGAAAGAGGTTGGAGGGGAAAGTTTACAAMapped 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|19052540|gb|BM731207.1|BM731207EST: GTGCCATTAATGGTGGTAAATATGTCTCCGTACATCTTCGTTTTGAAGAG GATATGGTTGCTTTCTCTTGTTGTGTTTTCGATGGTGGAAAACAGGAGAGA
genomic: GTGCCATTAATGGTGGTAAATATGTCTCCGTACATCTTCGTTTTGAAGAGgtttgttttg ... ccatgggcagGATATGGTTGCTTTCTCTTGTTGTGTTTTCGATGGTGGAAAACAGGAGAGA
EST:
gi|6134628|gb|AW133021.1|AW133021EST: GTGCCATTAATGGTGGTAAATATGTCTCCGTACATCTTCGTTTTGAAGAG GATATGGTTGCTTTCTCTTGTTGTGTTTTCGATGGTGGAAAACAGGAGAGA
genomic: GTGCCATTAATGGTGGTAAATATGTCTCCGTACATCTTCGTTTTGAAGAGgtttgttttg ... ccatgggcagGATATGGTTGCTTTCTCTTGTTGTGTTTTCGATGGTGGAAAACAGGAGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacgttgatatgttaatatttgttgcaactgatgcacatgatttcccatgggcagGATATGGTTGCTTTCTCTTGTTGTGTTTTCGATGGTGGAAAACAGGAGAGAGAAGACATGATTGCAGCTAGAGAAAGAGGTTGGAAAGGGAAATTTACAA
aactgat putative branch site (score: 3)
tttcccat putative PPT
atatgttaatatttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttttgatcagatatgaatatttatattaactttgaacgttgatatgttaatatttgttgcaactgatgcacatgatttcccatgggcagGATATGGTTGCTTTCTCTTGTTGTGTTTTCGATGGTGGAAAACAGGAGAGAGAAGACATGATTGCAGCTAGAGAAAGAGGTTGGAAAGGGAAATTTACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG