Sequence
atgc intronic sequence ATGC exonic sequence...gtgtgtgtttacatgtgagagaatgaatccttagttagcatagcatctttagttttgataacagctttatattttctttgtggtttaattatggatgcagCATGTGGAAGATCACCATTTATATTCATTGAATTACATGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG
Basic information
species | Glycine max |
transcript | GLYMA10G31510.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G31510.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g10770.1 (Oryza sativa), 3'ss of exon 6
---------gtgtgtgtttacatgtgagagaatgaatccttagttag----catagcatctttagttttgataac-----agctttatattttctttgt--ggtttaattatggatgc----agCATGTGGAAGATCACCATTTATATTCATTGAATTACATGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG
|||| || | ||| | | ||||| | | ||| || ||| | | | | |||| | || ||||| | | ||||||| ||||| || |||||||| ||| | || |||||||||||||| || ||||| |||||||||| || || ||||| ||||| || ||||||
gtaagatgcttgtgatattgcttgtcatgactttctgttctagttgtgcttcttgattcttttttttcccgaaactatccaacctgagatttgttacactcaattgtgttatgtctactaacagCATGTTGAAGACCATCATTTATACTCACTAAACTACATGCATTGGGGTGCCCCAAAGTTGTGGTATGGAGTTCCAGGAAAGGATGCTGTGAATTTGGAAT
upper sequence: GLYMA10G31510.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G156910_T01 (Zea mays), 3'ss of exon 6
----------------------------------gtgtgtgtttacatgtgagaga--atgaatccttagtta---gcatagcatctttagttttgataacagctttatattttctttgtggtttaattatggatgcagCATGTGGAAGATCACCATTTATATTCATTGAATTACATGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG
|| |||| || ||| | || ||| | ||| ||| | ||| | | | | |||| || | | | ||| | || || || |||||||| |||||||| ||||| || ||| |||| |||||||||||||| |||||||| ||||||||||| || || || || ||||| || ||||| |
gtaagatgcttttgatattctctttagtttcatagtttgtggttg-atgctattgattatggaagctttattatggacttagggtatcca-tcttga-aatatttcactgatttgaatttgaattgtgcctgttgacagCATGTTGAAGATCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTATGGAGTTCCAGGGAAGGATGCTGTGAATTTGGAGG
upper sequence: GLYMA10G31510.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G027075_T02 (Zea mays), 3'ss of exon 6
-----gtgtgtgtttacatgtg-agagaatgaatccttagttagcatagcatc-tttagttttgataac--agctttatattttctttgtggtttaattatggatgcagCATGTGGAAGATCACCATTTATATTCATTGAATTACATGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG
|| |||| ||||| | | | ||| | | ||| | | ||| | | | | | ||| ||| | | || |||||||| ||||| || ||||| || ||| |||| |||||||||||||| |||||||| ||||||||||| || || ||||| |||||| || ||||| |
gtaagatgcttgttggcatgtctacttctcttaccattaatattgttgtcattatccaaatttaacattcatgttctgagattttacactggcatgtctctgctgacagCATGTTGAAGACCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTATGGAGTTCCAGGAAAGGATGCCGTAAATTTGGAGG
upper sequence: GLYMA10G31510.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G140524_T02 (Zea mays), 3'ss of exon 7
-------------gtgtgtgtttacatgtgagagaatgaatcct-tagttagcatagcatctttagttttgataacagctttatattttctttgtggtttaattatggatgcagCATGTGGAAGATCACCATTTATATTCATTGAATTACATGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG-
| ||| ||| | | | ||| || | | || | || || |||| || || | | | ||| ||| | | || |||||||| ||||| || ||||| || ||| |||| |||||||||||||| |||||||| ||||||||||| || || ||||| ||||| || ||||| | ||
gtaagatgcttgttggcatgtctacttctcttacaattaagattgttgtcattatc-caaatttaacattcat----gttctgagattttacactggcatgtctctgctgacagCATGTTGAAGACCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTATGGAGTTCCAGGAAAGGATGC-TGTAAATTTGGAGG
upper sequence: GLYMA10G31510.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G08620.2 (Arabidopsis thaliana), 3'ss of exon 7
gtgtgtgtttacatgtgagagaatgaatccttagttagcatagcatcttt-agttttgataacagctttat---attttctttgtggtttaatta--tggatgcagCATGTGGAAGATCACCATTTATATTCATTGAATTACATGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG
| | | | | | | |||| || | | || || | || ||| | ||| | ||| ||| || ||| || || ||||||| ||||||||||| || ||||| |||||||| ||||| ||||| || || ||| ||||||||||||| || || ||||| ||| | || |
------atgcaattttcattacttcacatcttatttcgttttatattttccacttctgacattccttttgttctgctttttttttgtttttgtttacctgaaatagCATGTTGAAGATCACCACTTGTATTCGTTGAATTATATGCACTGGGGTGCACCGAAATTGTGGTATGGTGTTGGGGGGAAGGATGCTGTTAAACTCGAGG
upper sequence: GLYMA10G31510.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0036g00570.t01 (Vitis vinifera), 3'ss of exon 8
-gtgtgtgtttaca-tgtgagagaatgaatccttagttagcatagcatctttagttttgataacagctttatattttctttgtggtttaattatggatgcagCATGTGGAAGATCACCATTTATATTCATTGAATTACATGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG
|| | | | ||| | | ||| ||| | | | | | | ||| ||| | ||||| | || ||| |||| || || |||||||| |||||||| || |||||||| ||||| |||||||| ||||| ||||||||||| |||||||||||||| || |||||||| |||||||| |
agtatttaatgacacttttagatgttgattatgctgattcttttgtttatttg--tttatttgtttatttatttattttttcaaatttatttttgagaacagCATGTTGAAGATCATCACTTATATTCGTTGAACTACATGCACTGGGGTGCTCCAAAAATTTGGTATGGTGTCCCAGGGCAAGATGCCCTTAAATTGGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttagttttgataacagctttatattttctttgtggtttaattatggatgcagCATGTGGAAGATCACCATTTATATTCATTGAATTACATGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG
tttatattttctttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgtgtttacatgtgagagaatgaatccttagttagcatagcatctttagttttgataacagctttatattttctttgtggtttaattatggatgcagCATGTGGAAGATCACCATTTATATTCATTGAATTACATGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
gtgtgtg
- - - - - acatgtg