Sequence
atgc intronic sequence ATGC exonic sequencegtatgaactaaaaataataataaaatttttaaacaatatttttagtctaggaaaataaatcatactaatggaataaaaataatttgagtaactctattaattccattaattgaatagttactttttcctacgtaaaaattaaacatggcttattcaaatgttgaaacaataagccagATATCAGAGAAGGTGAAGCCACACCCGGTGGTGGTCAACATATTAACTAAAGTTGAAGATATAATCCCAAAGTGGAAGATAGTTCCCACAAAGGATGTCA
Basic information
species | Glycine max |
transcript | GLYMA03G37290.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G37290.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g21310.1 (Oryza sativa), 3'ss of exon 1
gtatgaactaaaaataataataaaatttttaaacaatatttttagtctaggaaaataaatcatactaatggaataaaaataatttgagtaactctattaattccattaattgaatagttactttttcctacgtaaaaattaaacatggcttattcaaatgttgaaacaataagccagATATCAGAGAAGGTGAAGCCACACCCGGTGGTGGTCAACATATTAACTAAAGTTGAAGATATAATCCCAAAGTGGAAGATAGTTCCCACAAAGGATGTCA
| | ||| | || | || | | | ||| ||| | | || | ||| | ||| | ||| | | | ||| || | | |||||||| |||||||||||||| |||||||||||| || | | || | || || || | ||||| | ||||||||| |||||||| ||||| ||||
-------------------------------------------------gtagctcgctgcatgcgcgtgcagaaatattcttctgaataatt----tgatctga------gaaaaatta---------agactgaaacttggtgcgtttccttccgatttgctggtgtt----cagATATCGGAGAAGGTGAAGCCGCACCCGGTGGTGATCTCTCTCCTGACGCAGGTAGAGGACGTCATCCCCAGGTGGAAGATTGTTCCCACCAAGGACGTCA
upper sequence: GLYMA03G37290.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G306851_T01 (Zea mays), 3'ss of exon 6
gtatgaactaaaaataataataaaatttttaaacaatatttttagtctaggaaaataaatcatactaatggaataaaaataatttgagtaactctattaattccattaattgaatagttactttttcctacgtaa--aaattaaac----atggcttattcaaa-tgttgaaacaataagccagATATCAGAGAAGGTGAAGCCACACCCGGTGGTGGTCAACATATTAACTAAAGTTGAAGATATAATCCCAAAGTGGAAGATAGTTCCCACAAAGGATGTCA
| || || | ||| || ||||||| |||| || | | || | || | |||||||| ||||| |||||||| |||||||||||||||| | | ||||| | || || || || ||||| ||||||||||| || ||||| ||||| ||||
---------------------------------------------------------------------------------------------------------------------gtgctattccatactgaacctgattaaactgtcatggtttctggagcctgcttgaatgacgttacagATATCGGAGAAAGTGAAGCCGCACCCGGTGGTGGTCACCCTGCTAACTCAGGTGGAGGAGATCATCCCCAAGTGGAAGATCGTCCCCACCAAGGACGTCA
upper sequence: GLYMA03G37290.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G62860.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgaactaaaaataataataaaatttttaaacaatatttttagtctaggaaaataaatcatactaatggaataaaaataatttgagtaactctattaattccattaattgaatagttactttttcctacgtaaaaattaaacatggcttattcaaatgttgaaacaataagccagATATCAGAGAAGGTGAAGCCACACCCGGTGGTGGTCAACATATTAACTAAAGTTGAAGATATAATCCCAAAGTGGAAGATAGTTCCCACAAAGGATGTCA
| | || | | || ||| | | ||| |||| | ||| | ||||| | | || ||| || || ||| | ||| | | ||| | || ||||||||||||||||||| |||||||| || || | || || |||| | |||||||||||| || ||||| |||||||||||||| ||||| ||||| |
------------------------------------------------gtcacgtttcttctcatctctatcatcgaaaccctatatttaatcaagttaagacacaaaatctattagtt-ttagacacaacttaattatcaa-catt-ttcatt--agttttgtgtgtgtgggc-agATATCAGAGAAGGTGAAACCACACCCAGTAGTCATAAATCTACTAACGAGAGTTGAAGATATTATACCAAAATGGAAGATAGTTCCTACAAAAGATGTTA
upper sequence: GLYMA03G37290.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G47630.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgaactaaaaataataataaaatttttaaacaatatttttagtctaggaaaataaatcatactaatggaataaaaataatttgagtaactctattaattccattaattgaatagttactttttcctacgtaaaaattaaacatggcttattcaaatgttgaaacaataagccagATATCAGAGAAGGTGAAGCCACACCCGGTGGTGGTCAACATATTAACTAAAGTTGAAGATATAATCCCAAAGTGGAAGATAGTTCCCACAAAGGATGTCA
||| || || ||| ||| | || | || | || | | | | |||| || | |||| ||||| ||| | |||||||| |||||||||||||||||||| | ||| | || | ||||||| ||| ||||| || || || || ||||| |||||||| ||||| || || |
--------------------------------------------------------------------------gtaaaaaacctg--caac--tataattttagattgcagagtcgtaggtgataataatattgaaat---gcaaagtatattgttatgtttaaata----tgcagATATCTGAGAAGGTGAAGCCACACCCTATAGTGATTAATCTGTTAACTAGAGTCGAAGAAATCATACCTAAATGGAAAATAGTTCCAACAAAAGACGTGA
upper sequence: GLYMA03G37290.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0005g00510.t01 (Vitis vinifera), 3'ss of exon 5
gtatgaactaaaaataataataaaatttttaaacaatatttttagtctaggaaaataaatcatactaatggaataaaaataatttgagtaac-tctattaattccattaattgaatagttactttttcctacgtaaaaattaaacatggcttattc--aaatgttgaaacaata-agccagATATCAGAGAAGGTGAAGCCACACCCGGTGGTGGTCAACATATTAACTAAAGTTGAAGATATAATCCCAAAGTGGAAGATAGTTCCCACAAAGGATGTCA
|||| || | ||| | | | | | | || || | || | | | | ||||| ||| ||| || ||||| ||| |||| | ||||| ||| | ||||| || | || | || | | |||||||| ||||||||||||||||| || || || || || |||||||| ||||| ||||| ||||| ||||||||||||||||| |||||||||||||| |
---------gtaaatg-caagatgattgtgtgatcaactcccaaattccacaacatgctttctattggttgga--------atttggaaaacatcttttttttccagc----------------tttgctaccaagaaattgaaccctgggtattcctaattaatgtatgaaaatggtcagATATCGGAGAAGGTGAAGCCACATCCTGTAGTTGTGAATATATTAACAAAAGTGGAAGAGATAATACCAAAGTGGAAGATAGTGCCCACAAAGGATGTAAMapped 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|17519393|gb|BM188435.1|BM188435EST: AGGACCCTTCATTCTGGGACGGTGCAGTTCTCGTCGCACCCATGTGTAAG ATATCAGAGAAGGTGAAGCCACACCCGGTGGTGGTCAACATATTAACTAAA
genomic: AGGACCCTTCATTCTGGGACGGTGCAGTTCTCGTCGCACCCATGTGTAAGgtatgaacta ... aataagccagATATCAGAGAAGGTGAAGCCACACCCGGTGGTGGTCAACATATTAACTAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcctacgtaaaaattaaacatggcttattcaaatgttgaaacaataagccagATATCAGAGAAGGTGAAGCCACACCCGGTGGTGGTCAACATATTAACTAAAGTTGAAGATATAATCCCAAAGTGGAAGATAGTTCCCACAAAGGATGTCA
taaaaattaaacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaactaaaaataataataaaatttttaaacaatatttttagtctaggaaaataaatcatactaatggaataaaaataatttgagtaactctattaattccattaattgaatagttactttttcctacgtaaaaattaaacatggcttattcaaatgttgaaacaataagccagATATCAGAGAAGGTGAAGCCACACCCGGTGGTGGTCAACATATTAACTAAAGTTGAAGATATAATCCCAAAGTGGAAGATAGTTCCCACAAAGGATGTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG