Sequence
atgc intronic sequence ATGC exonic sequence...gtatcaccgtgcttgacctttagaataataaccatcatttcctgataattttctattaactctcacttagaaaaagcatttcatagtgatttaactgcagACCGGCAATTGCATGGGCAACATGGGATCTTATAGCTATGGCTGAAAATGGAAGACATGATGGGCCTCCCACACATGCTGTCGTGTTTGTGTGGAATGGT
Basic information
species | Glycine max |
transcript | GLYMA19G11100.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G11100.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os08g29160.1 (Oryza sativa), 3'ss of exon 6
gtatcaccgtgcttgacctttagaataataaccatcatttcctgataattttctattaactctcacttagaaaaagcat----ttcatagtgatttaac--tgcagACCGGCAATTGCATGGGCAACATGGGATCTTATAGCTATGGCTGAAAATGGAAGACATGATGGGCCTCCCACACATGCTGTCGTGTTTGTGTGGAATGGT
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--------gtg-ttgttagttgacataattttcttaattgactgggcttgatccatctgcataagcagtgttgatccttaatgtccacatttgtctgaatatgcagAGCTGCAATTGTGTGGGCAACATGGGATCTCATTGCACTAGTTGAAAACGGAAGACATGATGGTACTCCCACACATTCAGTATGCTTTGTTTGGAACAGT
upper sequence: GLYMA19G11100.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G127374_T01 (Zea mays), 3'ss of exon 6
------------------------gtatcaccg--tgcttgacctttagaataataacc-atcat--ttcctgataattttctattaactctcacttagaaaaagcatttcatagtgatttaac--tgcagACCGGCAATTGCATGGGCAACATGGGATCTTATAGCTATGGCTGAAAATGGAAGACATGATGGGCCTCCCACACATGCTGTCGTGTTTGTGTGGAATGGT
| | ||||| | | | | | | | || ||| | || | || | | | | | || | | | ||| ||||| |||||| | ||||||| |||||||| ||||||||||| ||| | | |||||||||||| |||||||| |||||||||| | || || | ||||| ||
gtaattatggttgagcaaaaatatatcttgttagatgcttaatcaaagaggtggttgcttactgtgattgctgccacagttgtttttatggtta-tcggtttcagaactaaaaagtcgtttaatgatgcagAGCTGCAATTGTTTGGGCAACTTGGGATCTTATTGCTTTAGTTGAAAATGGAAGGCATGATGGTAGTCCCACACATTCAGTTTGTTTCATTTGGAACAGT
upper sequence: GLYMA19G11100.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G01510.1 (Arabidopsis thaliana), 3'ss of exon 6
----gtatcaccgtgcttgacctttagaataataaccatcatttcctgataattttctattaactctcacttagaaaaagcatttcatagtgatttaactgcagACCGGCAATTGCATGGGCAACATGGGATCTTATAGCTATGGCTGAAAATGGAAGACATGATGGGCCTCCCACACATGCTGTCGTGTTTGTGTGGAATGGT
|||| | | | | || | ||||| || | || | || | | | | | | || | ||| |||| |||||| |||||||| |||||||||||||||||||| ||||||| || |||| | |||||||||| |||| ||||| |||| ||||||||||||||
gtttttatccatcttatctctgtcttgaccattaacctgcagaccatggatagcttttctgttttaatgaaaacatcagacaagttatatgtattttttcacagACCTGCAATTGCTTGGGCAACATGGGATCTTATCGCTATGGTGGACGATGGCAAACATGATGGGACTCCAACACACTCTGTAACCTTTGTGTGGAATGGA
upper sequence: GLYMA19G11100.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv14s0066g01200.t01 (Vitis vinifera), 3'ss of exon 6
--gtatcaccgtgcttgacctttagaataataaccatcatttcctgataattttctattaactctcacttagaaaaagcatttcatagtgatttaactgcagACCGGCAATTGCATGGGCAACATGGGATCTTATAGCTATGGCTGAAAATGGAAGACATGATGGGCCTCCCACACATGCTGTCGTGTTTGTGTGGAATGGT
| | || | | || | || ||| |||| || | || || | | | | | ||| ||| || | | | | |||||||| |||||||| |||||||| |||||||||||||| |||| ||||| || | ||| ||||||||| | || |||||||| ||||||||||||||
aaagaaaaaagtaca-gtactgaactatggtaaacatctttaggaagaagttggttactgataaaaattgacaaattatattg-atggaactctgaatgcagACCAGCAATTGCTTGGGCAACGTGGGATCTTATAGCCATGGTCGAAAAAGGCAAACACGATGGGCCTGCAACCCATGCTGTGACCTTTGTGTGGAATGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taattttctattaactctcacttagaaaaagcatttcatagtgatttaactgcagACCGGCAATTGCATGGGCAACATGGGATCTTATAGCTATGGCTGAAAATGGAAGACATGATGGGCCTCCCACACATGCTGTCGTGTTTGTGTGGAATGGT
ttctattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcaccgtgcttgacctttagaataataaccatcatttcctgataattttctattaactctcacttagaaaaagcatttcatagtgatttaactgcagACCGGCAATTGCATGGGCAACATGGGATCTTATAGCTATGGCTGAAAATGGAAGACATGATGGGCCTCCCACACATGCTGTCGTGTTTGTGTGGAATGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - -accgtgc
- - - - - - - - - - - - - - - -ccatcat
- - - - - - - - - - - - - - - - - - - - cctgata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatttc